HEADER HYDROLASE/HYDROLASE INHIBITOR 03-FEB-17 5N0Z
TITLE HPAD4 CRYSTAL COMPLEX WITH AFM-41A
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEIN-ARGININE DEIMINASE TYPE-4;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: HL-60 PAD,PEPTIDYLARGININE DEIMINASE IV,PROTEIN-ARGININE
COMPND 5 DEIMINASE TYPE IV;
COMPND 6 EC: 3.5.3.15;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: PADI4, PAD4, PADI5, PDI5;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR E.BEAUMONT,P.KERRY,P.THOMPSON,A.MUTH,V.SUBRAMANIAN,M.NAGAR,H.SRINATH,
AUTHOR 2 K.CLANCY,S.PARELKAR
REVDAT 1 24-MAY-17 5N0Z 0
JRNL AUTH A.MUTH,V.SUBRAMANIAN,E.BEAUMONT,M.NAGAR,P.KERRY,P.MCEWAN,
JRNL AUTH 2 H.SRINATH,K.CLANCY,S.PARELKAR,P.R.THOMPSON
JRNL TITL DEVELOPMENT OF A SELECTIVE INHIBITOR OF PROTEIN ARGININE
JRNL TITL 2 DEIMINASE 2.
JRNL REF J. MED. CHEM. V. 60 3198 2017
JRNL REFN ISSN 1520-4804
JRNL PMID 28328217
JRNL DOI 10.1021/ACS.JMEDCHEM.7B00274
REMARK 2
REMARK 2 RESOLUTION. 2.52 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0158
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.52
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.79
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 3 NUMBER OF REFLECTIONS : 26964
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.183
REMARK 3 R VALUE (WORKING SET) : 0.180
REMARK 3 FREE R VALUE : 0.229
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1412
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.52
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.59
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1962
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.43
REMARK 3 BIN R VALUE (WORKING SET) : 0.3730
REMARK 3 BIN FREE R VALUE SET COUNT : 108
REMARK 3 BIN FREE R VALUE : 0.4340
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5024
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 50
REMARK 3 SOLVENT ATOMS : 196
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.64
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -2.43000
REMARK 3 B22 (A**2) : 9.81000
REMARK 3 B33 (A**2) : -1.55000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -3.14000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.440
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.261
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.252
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.041
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5199 ; 0.013 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 4791 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7060 ; 1.706 ; 1.978
REMARK 3 BOND ANGLES OTHERS (DEGREES): 11175 ; 1.033 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 636 ; 7.395 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 226 ;35.840 ;24.646
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 887 ;15.701 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;14.313 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 782 ; 0.088 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5738 ; 0.008 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1012 ; 0.002 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2553 ; 3.980 ; 5.356
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2552 ; 3.981 ; 5.356
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3186 ; 6.286 ; 8.012
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3187 ; 6.285 ; 8.012
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2646 ; 4.005 ; 5.755
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2647 ; 4.004 ; 5.755
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3875 ; 6.422 ; 8.452
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 23081 ;10.898 ;99.245
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 23082 ;10.898 ;99.244
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 5N0Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-FEB-17.
REMARK 100 THE DEPOSITION ID IS D_1200003383.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 23-NOV-15
REMARK 200 TEMPERATURE (KELVIN) : 173
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I04
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28377
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.520
REMARK 200 RESOLUTION RANGE LOW (A) : 55.790
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 200 DATA REDUNDANCY : 3.400
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.52
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6
REMARK 200 DATA REDUNDANCY IN SHELL : 3.40
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.71
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M IMIDAZOLE PH7.5, 0.2MM LISO4, 8
REMARK 280 -11% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 73.57500
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.47000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 73.57500
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.47000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 6350 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 51550 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -152.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLY A -6
REMARK 465 PRO A -5
REMARK 465 LEU A -4
REMARK 465 GLY A -3
REMARK 465 SER A -2
REMARK 465 PRO A -1
REMARK 465 GLN A 0
REMARK 465 MET A 1
REMARK 465 ALA A 2
REMARK 465 SER A 55
REMARK 465 PRO A 56
REMARK 465 PRO A 57
REMARK 465 ALA A 58
REMARK 465 LYS A 59
REMARK 465 LYS A 60
REMARK 465 LYS A 61
REMARK 465 SER A 62
REMARK 465 THR A 63
REMARK 465 GLY A 64
REMARK 465 SER A 65
REMARK 465 PRO A 129
REMARK 465 THR A 130
REMARK 465 ARG A 131
REMARK 465 ALA A 132
REMARK 465 VAL A 133
REMARK 465 LYS A 134
REMARK 465 ARG A 218
REMARK 465 GLY A 219
REMARK 465 LYS A 220
REMARK 465 LEU A 221
REMARK 465 SER A 222
REMARK 465 SER A 223
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG A 205 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES
REMARK 500 ARG A 427 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 SER A 32 13.86 -141.22
REMARK 500 ASP A 36 1.56 85.42
REMARK 500 ARG A 123 48.27 75.21
REMARK 500 ASN A 158 109.06 -54.00
REMARK 500 SER A 161 -169.76 -107.87
REMARK 500 ASP A 209 3.93 -67.53
REMARK 500 ASP A 344 -4.95 84.70
REMARK 500 ARG A 374 -158.73 -93.58
REMARK 500 LYS A 377 -37.58 -38.30
REMARK 500 GLN A 455 -58.80 68.09
REMARK 500 ALA A 458 69.98 38.18
REMARK 500 ARG A 484 -126.63 51.95
REMARK 500 CYS A 610 115.64 -37.17
REMARK 500 HIS A 640 24.43 82.71
REMARK 500 GLU A 642 -156.99 -126.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 705 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN A 153 OD1
REMARK 620 2 ASP A 155 OD1 93.6
REMARK 620 3 ASP A 157 OD2 156.2 94.9
REMARK 620 4 ASP A 165 OD2 106.6 80.2 96.7
REMARK 620 5 ASP A 176 OD1 85.0 154.3 96.7 75.6
REMARK 620 6 ASP A 179 OD2 90.9 90.7 66.8 160.6 115.0
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 706 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 155 OD2
REMARK 620 2 ASP A 157 OD1 88.0
REMARK 620 3 ASP A 157 OD2 93.3 45.1
REMARK 620 4 ASP A 179 OD1 105.4 154.4 111.2
REMARK 620 5 ASP A 179 OD2 80.1 112.2 69.0 51.3
REMARK 620 6 ASP A 388 OD1 110.8 82.2 121.6 111.9 162.8
REMARK 620 7 HOH A 901 O 161.1 81.9 68.3 78.8 88.9 83.7
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 707 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 165 O
REMARK 620 2 ASP A 168 OD1 77.3
REMARK 620 3 GLU A 170 O 165.5 88.3
REMARK 620 4 HOH A 905 O 79.4 82.8 97.8
REMARK 620 5 HOH A 825 O 95.1 147.7 97.8 127.2
REMARK 620 6 HOH A 858 O 86.0 67.6 89.6 149.2 80.7
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 703 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLN A 349 OE1
REMARK 620 2 GLU A 353 OE1 133.1
REMARK 620 3 PHE A 407 O 82.6 96.9
REMARK 620 4 LEU A 410 O 146.4 78.9 83.5
REMARK 620 5 GLU A 411 OE1 83.6 139.7 105.1 70.7
REMARK 620 6 HOH A 943 O 100.2 83.6 175.6 92.3 72.0
REMARK 620 7 HOH A 822 O 67.5 67.9 72.0 135.2 151.2 112.2
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 704 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 351 OE1
REMARK 620 2 ASP A 369 OD1 103.3
REMARK 620 3 SER A 370 O 87.5 79.5
REMARK 620 4 ASN A 373 OD1 84.6 171.1 97.1
REMARK 620 5 HOH A 924 O 162.8 83.5 78.2 87.8
REMARK 620 6 HOH A 808 O 104.4 91.3 166.5 90.6 91.1
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 701
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 702
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 703
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 704
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 705
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 706
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 707
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 8FT A 708
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5N0M RELATED DB: PDB
REMARK 900 RELATED ID: 5N0Y RELATED DB: PDB
DBREF 5N0Z A 1 663 UNP Q9UM07 PADI4_HUMAN 1 663
SEQADV 5N0Z GLY A -6 UNP Q9UM07 EXPRESSION TAG
SEQADV 5N0Z PRO A -5 UNP Q9UM07 EXPRESSION TAG
SEQADV 5N0Z LEU A -4 UNP Q9UM07 EXPRESSION TAG
SEQADV 5N0Z GLY A -3 UNP Q9UM07 EXPRESSION TAG
SEQADV 5N0Z SER A -2 UNP Q9UM07 EXPRESSION TAG
SEQADV 5N0Z PRO A -1 UNP Q9UM07 EXPRESSION TAG
SEQADV 5N0Z GLN A 0 UNP Q9UM07 EXPRESSION TAG
SEQADV 5N0Z SER A 55 UNP Q9UM07 GLY 55 ENGINEERED MUTATION
SEQADV 5N0Z ALA A 82 UNP Q9UM07 VAL 82 ENGINEERED MUTATION
SEQADV 5N0Z ALA A 112 UNP Q9UM07 GLY 112 ENGINEERED MUTATION
SEQRES 1 A 670 GLY PRO LEU GLY SER PRO GLN MET ALA GLN GLY THR LEU
SEQRES 2 A 670 ILE ARG VAL THR PRO GLU GLN PRO THR HIS ALA VAL CYS
SEQRES 3 A 670 VAL LEU GLY THR LEU THR GLN LEU ASP ILE CYS SER SER
SEQRES 4 A 670 ALA PRO GLU ASP CYS THR SER PHE SER ILE ASN ALA SER
SEQRES 5 A 670 PRO GLY VAL VAL VAL ASP ILE ALA HIS SER PRO PRO ALA
SEQRES 6 A 670 LYS LYS LYS SER THR GLY SER SER THR TRP PRO LEU ASP
SEQRES 7 A 670 PRO GLY VAL GLU VAL THR LEU THR MET LYS ALA ALA SER
SEQRES 8 A 670 GLY SER THR GLY ASP GLN LYS VAL GLN ILE SER TYR TYR
SEQRES 9 A 670 GLY PRO LYS THR PRO PRO VAL LYS ALA LEU LEU TYR LEU
SEQRES 10 A 670 THR ALA VAL GLU ILE SER LEU CYS ALA ASP ILE THR ARG
SEQRES 11 A 670 THR GLY LYS VAL LYS PRO THR ARG ALA VAL LYS ASP GLN
SEQRES 12 A 670 ARG THR TRP THR TRP GLY PRO CYS GLY GLN GLY ALA ILE
SEQRES 13 A 670 LEU LEU VAL ASN CYS ASP ARG ASP ASN LEU GLU SER SER
SEQRES 14 A 670 ALA MET ASP CYS GLU ASP ASP GLU VAL LEU ASP SER GLU
SEQRES 15 A 670 ASP LEU GLN ASP MET SER LEU MET THR LEU SER THR LYS
SEQRES 16 A 670 THR PRO LYS ASP PHE PHE THR ASN HIS THR LEU VAL LEU
SEQRES 17 A 670 HIS VAL ALA ARG SER GLU MET ASP LYS VAL ARG VAL PHE
SEQRES 18 A 670 GLN ALA THR ARG GLY LYS LEU SER SER LYS CYS SER VAL
SEQRES 19 A 670 VAL LEU GLY PRO LYS TRP PRO SER HIS TYR LEU MET VAL
SEQRES 20 A 670 PRO GLY GLY LYS HIS ASN MET ASP PHE TYR VAL GLU ALA
SEQRES 21 A 670 LEU ALA PHE PRO ASP THR ASP PHE PRO GLY LEU ILE THR
SEQRES 22 A 670 LEU THR ILE SER LEU LEU ASP THR SER ASN LEU GLU LEU
SEQRES 23 A 670 PRO GLU ALA VAL VAL PHE GLN ASP SER VAL VAL PHE ARG
SEQRES 24 A 670 VAL ALA PRO TRP ILE MET THR PRO ASN THR GLN PRO PRO
SEQRES 25 A 670 GLN GLU VAL TYR ALA CYS SER ILE PHE GLU ASN GLU ASP
SEQRES 26 A 670 PHE LEU LYS SER VAL THR THR LEU ALA MET LYS ALA LYS
SEQRES 27 A 670 CYS LYS LEU THR ILE CYS PRO GLU GLU GLU ASN MET ASP
SEQRES 28 A 670 ASP GLN TRP MET GLN ASP GLU MET GLU ILE GLY TYR ILE
SEQRES 29 A 670 GLN ALA PRO HIS LYS THR LEU PRO VAL VAL PHE ASP SER
SEQRES 30 A 670 PRO ARG ASN ARG GLY LEU LYS GLU PHE PRO ILE LYS ARG
SEQRES 31 A 670 VAL MET GLY PRO ASP PHE GLY TYR VAL THR ARG GLY PRO
SEQRES 32 A 670 GLN THR GLY GLY ILE SER GLY LEU ASP SER PHE GLY ASN
SEQRES 33 A 670 LEU GLU VAL SER PRO PRO VAL THR VAL ARG GLY LYS GLU
SEQRES 34 A 670 TYR PRO LEU GLY ARG ILE LEU PHE GLY ASP SER CYS TYR
SEQRES 35 A 670 PRO SER ASN ASP SER ARG GLN MET HIS GLN ALA LEU GLN
SEQRES 36 A 670 ASP PHE LEU SER ALA GLN GLN VAL GLN ALA PRO VAL LYS
SEQRES 37 A 670 LEU TYR SER ASP TRP LEU SER VAL GLY HIS VAL ASP GLU
SEQRES 38 A 670 PHE LEU SER PHE VAL PRO ALA PRO ASP ARG LYS GLY PHE
SEQRES 39 A 670 ARG LEU LEU LEU ALA SER PRO ARG SER CYS TYR LYS LEU
SEQRES 40 A 670 PHE GLN GLU GLN GLN ASN GLU GLY HIS GLY GLU ALA LEU
SEQRES 41 A 670 LEU PHE GLU GLY ILE LYS LYS LYS LYS GLN GLN LYS ILE
SEQRES 42 A 670 LYS ASN ILE LEU SER ASN LYS THR LEU ARG GLU HIS ASN
SEQRES 43 A 670 SER PHE VAL GLU ARG CYS ILE ASP TRP ASN ARG GLU LEU
SEQRES 44 A 670 LEU LYS ARG GLU LEU GLY LEU ALA GLU SER ASP ILE ILE
SEQRES 45 A 670 ASP ILE PRO GLN LEU PHE LYS LEU LYS GLU PHE SER LYS
SEQRES 46 A 670 ALA GLU ALA PHE PHE PRO ASN MET VAL ASN MET LEU VAL
SEQRES 47 A 670 LEU GLY LYS HIS LEU GLY ILE PRO LYS PRO PHE GLY PRO
SEQRES 48 A 670 VAL ILE ASN GLY ARG CYS CYS LEU GLU GLU LYS VAL CYS
SEQRES 49 A 670 SER LEU LEU GLU PRO LEU GLY LEU GLN CYS THR PHE ILE
SEQRES 50 A 670 ASN ASP PHE PHE THR TYR HIS ILE ARG HIS GLY GLU VAL
SEQRES 51 A 670 HIS CYS GLY THR ASN VAL ARG ARG LYS PRO PHE SER PHE
SEQRES 52 A 670 LYS TRP TRP ASN MET VAL PRO
HET SO4 A 701 5
HET SO4 A 702 5
HET CA A 703 1
HET CA A 704 1
HET CA A 705 1
HET CA A 706 1
HET CA A 707 1
HET 8FT A 708 35
HETNAM SO4 SULFATE ION
HETNAM CA CALCIUM ION
HETNAM 8FT 2-ETHYL-~{N}-[(1~{S})-4-(2-FLUORANYLETHANIMIDOYLAMINO)-
HETNAM 2 8FT 1-(4-METHOXY-1-METHYL-BENZIMIDAZOL-2-YL)BUTYL]-3-
HETNAM 3 8FT OXIDANYLIDENE-1~{H}-ISOINDOLE-4-CARBOXAMIDE
FORMUL 2 SO4 2(O4 S 2-)
FORMUL 4 CA 5(CA 2+)
FORMUL 9 8FT C26 H31 F N6 O3
FORMUL 10 HOH *196(H2 O)
HELIX 1 AA1 MET A 164 ASP A 168 5 5
HELIX 2 AA2 SER A 174 ASP A 179 5 6
HELIX 3 AA3 ASP A 192 THR A 195 5 4
HELIX 4 AA4 ALA A 204 ASP A 209 1 6
HELIX 5 AA5 ASN A 316 ALA A 330 1 15
HELIX 6 AA6 PRO A 338 MET A 343 1 6
HELIX 7 AA7 TRP A 347 GLU A 351 1 5
HELIX 8 AA8 GLU A 378 ARG A 383 1 6
HELIX 9 AA9 SER A 402 GLY A 408 5 7
HELIX 10 AB1 HIS A 444 GLN A 454 1 11
HELIX 11 AB2 HIS A 471 GLU A 474 5 4
HELIX 12 AB3 PRO A 494 GLU A 507 1 14
HELIX 13 AB4 GLY A 508 GLU A 511 5 4
HELIX 14 AB5 ILE A 526 SER A 531 1 6
HELIX 15 AB6 ASN A 532 GLY A 558 1 27
HELIX 16 AB7 ALA A 560 SER A 562 5 3
HELIX 17 AB8 CYS A 611 GLU A 621 1 11
HELIX 18 AB9 PRO A 622 GLY A 624 5 3
HELIX 19 AC1 TYR A 636 HIS A 640 5 5
HELIX 20 AC2 GLU A 642 GLY A 646 1 5
HELIX 21 AC3 LYS A 657 MET A 661 5 5
SHEET 1 AA1 4 GLY A 4 ARG A 8 0
SHEET 2 AA1 4 LEU A 24 ASP A 28 1 O GLN A 26 N ILE A 7
SHEET 3 AA1 4 GLU A 75 MET A 80 -1 O VAL A 76 N LEU A 27
SHEET 4 AA1 4 VAL A 48 ALA A 53 -1 N VAL A 49 O THR A 79
SHEET 1 AA2 5 THR A 15 VAL A 20 0
SHEET 2 AA2 5 THR A 101 ALA A 119 1 O TYR A 109 N THR A 15
SHEET 3 AA2 5 GLN A 90 GLY A 98 -1 N ILE A 94 O ALA A 106
SHEET 4 AA2 5 SER A 39 ALA A 44 -1 N SER A 41 O SER A 95
SHEET 5 AA2 5 TRP A 68 PRO A 69 -1 O TRP A 68 N PHE A 40
SHEET 1 AA3 6 THR A 15 VAL A 20 0
SHEET 2 AA3 6 THR A 101 ALA A 119 1 O TYR A 109 N THR A 15
SHEET 3 AA3 6 SER A 181 THR A 189 -1 O THR A 184 N CYS A 118
SHEET 4 AA3 6 GLY A 243 ALA A 253 -1 O GLY A 243 N THR A 189
SHEET 5 AA3 6 VAL A 211 ALA A 216 -1 N PHE A 214 O TYR A 250
SHEET 6 AA3 6 SER A 226 LEU A 229 -1 O VAL A 228 N VAL A 213
SHEET 1 AA4 5 ALA A 148 LEU A 150 0
SHEET 2 AA4 5 ALA A 282 VAL A 293 1 O ARG A 292 N LEU A 150
SHEET 3 AA4 5 LEU A 264 ASP A 273 -1 N LEU A 271 O VAL A 284
SHEET 4 AA4 5 HIS A 197 HIS A 202 -1 N HIS A 202 O THR A 268
SHEET 5 AA4 5 SER A 235 LEU A 238 -1 O LEU A 238 N LEU A 199
SHEET 1 AA5 3 LYS A 333 CYS A 337 0
SHEET 2 AA5 3 PRO A 305 CYS A 311 1 N GLN A 306 O LYS A 333
SHEET 3 AA5 3 THR A 647 ARG A 651 -1 O ASN A 648 N TYR A 309
SHEET 1 AA6 3 MET A 352 ALA A 359 0
SHEET 2 AA6 3 LYS A 362 ASP A 369 -1 O PHE A 368 N GLU A 353
SHEET 3 AA6 3 GLY A 390 THR A 393 1 O GLY A 390 N PRO A 365
SHEET 1 AA7 3 LEU A 410 VAL A 412 0
SHEET 2 AA7 3 ILE A 428 ASP A 432 -1 O LEU A 429 N GLU A 411
SHEET 3 AA7 3 VAL A 460 TYR A 463 1 O LEU A 462 N PHE A 430
SHEET 1 AA8 2 VAL A 416 VAL A 418 0
SHEET 2 AA8 2 LYS A 421 TYR A 423 -1 O LYS A 421 N VAL A 418
SHEET 1 AA9 3 LEU A 476 PRO A 480 0
SHEET 2 AA9 3 PHE A 487 SER A 493 -1 O LEU A 490 N SER A 477
SHEET 3 AA9 3 ILE A 564 PRO A 568 1 O ILE A 565 N LEU A 489
SHEET 1 AB1 2 LEU A 513 LEU A 514 0
SHEET 2 AB1 2 GLN A 524 LYS A 525 -1 O GLN A 524 N LEU A 514
SHEET 1 AB2 2 PHE A 571 LEU A 573 0
SHEET 2 AB2 2 ALA A 579 ALA A 581 -1 O GLU A 580 N LYS A 572
SHEET 1 AB3 3 LEU A 590 LEU A 592 0
SHEET 2 AB3 3 HIS A 595 PRO A 599 -1 O HIS A 595 N LEU A 592
SHEET 3 AB3 3 GLN A 626 ILE A 630 1 O ILE A 630 N ILE A 598
SHEET 1 AB4 2 VAL A 605 ILE A 606 0
SHEET 2 AB4 2 ARG A 609 CYS A 610 -1 O ARG A 609 N ILE A 606
LINK OD1 ASN A 153 CA CA A 705 1555 1555 2.55
LINK OD1 ASP A 155 CA CA A 705 1555 1555 2.39
LINK OD2 ASP A 155 CA CA A 706 1555 1555 2.32
LINK OD1 ASP A 157 CA CA A 706 1555 1555 2.96
LINK OD2 ASP A 157 CA CA A 706 1555 1555 2.62
LINK OD2 ASP A 157 CA CA A 705 1555 1555 2.79
LINK O ASP A 165 CA CA A 707 1555 1555 2.30
LINK OD2 ASP A 165 CA CA A 705 1555 1555 2.07
LINK OD1 ASP A 168 CA CA A 707 1555 1555 2.43
LINK O GLU A 170 CA CA A 707 1555 1555 2.27
LINK OD1 ASP A 176 CA CA A 705 1555 1555 2.48
LINK OD1 ASP A 179 CA CA A 706 1555 1555 2.73
LINK OD2 ASP A 179 CA CA A 706 1555 1555 2.35
LINK OD2 ASP A 179 CA CA A 705 1555 1555 2.28
LINK OE1 GLN A 349 CA CA A 703 1555 1555 2.37
LINK OE1 GLU A 351 CA CA A 704 1555 1555 2.53
LINK OE1 GLU A 353 CA CA A 703 1555 1555 2.48
LINK OD1 ASP A 369 CA CA A 704 1555 1555 2.54
LINK O SER A 370 CA CA A 704 1555 1555 2.35
LINK OD1 ASN A 373 CA CA A 704 1555 1555 2.33
LINK OD1 ASP A 388 CA CA A 706 1555 1555 2.34
LINK O PHE A 407 CA CA A 703 1555 1555 2.33
LINK O LEU A 410 CA CA A 703 1555 1555 2.51
LINK OE1 GLU A 411 CA CA A 703 1555 1555 2.53
LINK SG CYS A 645 C20 8FT A 708 1555 1555 1.64
LINK CA CA A 703 O HOH A 943 1555 1555 2.59
LINK CA CA A 703 O HOH A 822 1555 1555 2.66
LINK CA CA A 704 O HOH A 924 1555 1555 2.33
LINK CA CA A 704 O HOH A 808 1555 1555 2.17
LINK CA CA A 706 O HOH A 901 1555 1555 2.36
LINK CA CA A 707 O HOH A 905 1555 1555 2.49
LINK CA CA A 707 O HOH A 825 1555 1555 2.04
LINK CA CA A 707 O HOH A 858 1555 1555 2.48
SITE 1 AC1 4 SER A 402 GLY A 403 ARG A 441 8FT A 708
SITE 1 AC2 3 LYS A 525 LYS A 527 ASN A 528
SITE 1 AC3 7 GLN A 349 GLU A 353 PHE A 407 LEU A 410
SITE 2 AC3 7 GLU A 411 HOH A 822 HOH A 943
SITE 1 AC4 6 GLU A 351 ASP A 369 SER A 370 ASN A 373
SITE 2 AC4 6 HOH A 808 HOH A 924
SITE 1 AC5 6 ASN A 153 ASP A 155 ASP A 157 ASP A 165
SITE 2 AC5 6 ASP A 176 ASP A 179
SITE 1 AC6 5 ASP A 155 ASP A 157 ASP A 179 ASP A 388
SITE 2 AC6 5 HOH A 901
SITE 1 AC7 6 ASP A 165 ASP A 168 GLU A 170 HOH A 825
SITE 2 AC7 6 HOH A 858 HOH A 905
SITE 1 AC8 11 TRP A 347 ASP A 350 ARG A 374 GLY A 408
SITE 2 AC8 11 VAL A 469 HIS A 471 ASP A 473 ARG A 639
SITE 3 AC8 11 CYS A 645 SO4 A 701 HOH A 820
CRYST1 147.150 60.940 115.320 90.00 124.68 90.00 C 1 2 1 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.006796 0.000000 0.004702 0.00000
SCALE2 0.000000 0.016410 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010545 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
