HEADER HYDROLASE 03-OCT-17 5YIB
TITLE CRYSTAL STRUCTURE OF KNI-10743 BOUND PLASMEPSIN II (PMII) FROM
TITLE 2 PLASMODIUM FALCIPARUM
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PLASMEPSIN II;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 126-453;
COMPND 5 EC: 3.4.23.39;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM;
SOURCE 3 ORGANISM_COMMON: ISOLATE 3D7;
SOURCE 4 ORGANISM_TAXID: 36329;
SOURCE 5 GENE: PF14_0077, PF3D7_1408000;
SOURCE 6 EXPRESSION_SYSTEM: ENTEROBACTERIA PHAGE L1;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 268588
KEYWDS PLASMEPSIN, PLASMEPSIN II, KNI-10743, ASPARTIC PROTEASE, PLASMODIUM
KEYWDS 2 FALCIPARUM, DRUG DEVELOPMENT, INHIBITOR, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR I.RATHORE,V.MISHRA,P.BHAUMIK
REVDAT 3 29-MAY-19 5YIB 1 JRNL
REVDAT 2 18-JUL-18 5YIB 1 JRNL
REVDAT 1 11-JUL-18 5YIB 0
JRNL AUTH V.MISHRA,I.RATHORE,A.AREKAR,L.K.STHANAM,H.XIAO,Y.KISO,S.SEN,
JRNL AUTH 2 S.PATANKAR,A.GUSTCHINA,K.HIDAKA,A.WLODAWER,R.Y.YADA,
JRNL AUTH 3 P.BHAUMIK
JRNL TITL DECIPHERING THE MECHANISM OF POTENT PEPTIDOMIMETIC
JRNL TITL 2 INHIBITORS TARGETING PLASMEPSINS - BIOCHEMICAL AND
JRNL TITL 3 STRUCTURAL INSIGHTS.
JRNL REF FEBS J. V. 285 3077 2018
JRNL REFN ISSN 1742-464X
JRNL PMID 29943906
JRNL DOI 10.1111/FEBS.14598
REMARK 2
REMARK 2 RESOLUTION. 2.15 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0103
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 20484
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) : 0.179
REMARK 3 R VALUE (WORKING SET) : 0.178
REMARK 3 FREE R VALUE : 0.196
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1078
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) : 2.15
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1519
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88
REMARK 3 BIN R VALUE (WORKING SET) : 0.3010
REMARK 3 BIN FREE R VALUE SET COUNT : 80
REMARK 3 BIN FREE R VALUE : 0.3640
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2600
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 121
REMARK 3 SOLVENT ATOMS : 114
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.45
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.98000
REMARK 3 B22 (A**2) : -0.98000
REMARK 3 B33 (A**2) : 1.96000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.219
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.161
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.128
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.802
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2817 ; 0.010 ; 0.020
REMARK 3 BOND LENGTHS OTHERS (A): 2627 ; 0.006 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3840 ; 1.529 ; 2.003
REMARK 3 BOND ANGLES OTHERS (DEGREES): 6077 ; 0.938 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 335 ; 6.921 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;39.821 ;25.600
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 441 ;15.859 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;24.711 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 434 ; 0.086 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3117 ; 0.005 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 629 ; 0.001 ; 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): 1319 ; 1.159 ; 2.922
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1318 ; 1.159 ; 2.921
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1649 ; 1.966 ; 4.378
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1650 ; 1.965 ; 4.379
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1498 ; 1.481 ; 3.286
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1499 ; 1.480 ; 3.288
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2188 ; 2.460 ; 4.830
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3010 ; 5.351 ;24.570
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3011 ; 5.351 ;24.582
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 : 3
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 4 A 17
REMARK 3 ORIGIN FOR THE GROUP (A): 10.9486 -39.2140 -13.4602
REMARK 3 T TENSOR
REMARK 3 T11: 0.2231 T22: 0.2296
REMARK 3 T33: 0.1628 T12: -0.0268
REMARK 3 T13: 0.0859 T23: 0.0429
REMARK 3 L TENSOR
REMARK 3 L11: 4.4912 L22: 7.7720
REMARK 3 L33: 12.1643 L12: -3.4456
REMARK 3 L13: -3.0411 L23: 4.2874
REMARK 3 S TENSOR
REMARK 3 S11: 0.1315 S12: -0.7101 S13: -0.1160
REMARK 3 S21: 0.5612 S22: 0.0874 S23: 0.2130
REMARK 3 S31: -0.3145 S32: -0.0832 S33: -0.2189
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 18 A 220
REMARK 3 ORIGIN FOR THE GROUP (A): 20.3843 -36.2623 -20.6624
REMARK 3 T TENSOR
REMARK 3 T11: 0.1849 T22: 0.1005
REMARK 3 T33: 0.1043 T12: 0.0139
REMARK 3 T13: 0.0350 T23: 0.0272
REMARK 3 L TENSOR
REMARK 3 L11: 2.8217 L22: 1.6096
REMARK 3 L33: 1.5778 L12: -0.7424
REMARK 3 L13: 1.0318 L23: -0.1433
REMARK 3 S TENSOR
REMARK 3 S11: -0.0159 S12: -0.0347 S13: -0.2054
REMARK 3 S21: 0.1138 S22: -0.0501 S23: 0.0574
REMARK 3 S31: 0.1536 S32: 0.1171 S33: 0.0660
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 221 A 331
REMARK 3 ORIGIN FOR THE GROUP (A): 1.6124 -25.1126 -23.7880
REMARK 3 T TENSOR
REMARK 3 T11: 0.0879 T22: 0.0945
REMARK 3 T33: 0.1831 T12: -0.0144
REMARK 3 T13: 0.0167 T23: 0.0237
REMARK 3 L TENSOR
REMARK 3 L11: 1.8864 L22: 2.7846
REMARK 3 L33: 1.5047 L12: -1.2992
REMARK 3 L13: -0.6996 L23: 0.9035
REMARK 3 S TENSOR
REMARK 3 S11: 0.0692 S12: 0.1206 S13: -0.3024
REMARK 3 S21: 0.0265 S22: -0.1032 S23: 0.4402
REMARK 3 S31: 0.0470 S32: -0.1530 S33: 0.0340
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 5YIB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-OCT-17.
REMARK 100 THE DEPOSITION ID IS D_1300005324.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-MAY-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54182
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21566
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150
REMARK 200 RESOLUTION RANGE LOW (A) : 40.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 7.300
REMARK 200 R MERGE (I) : 0.08700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 6.90
REMARK 200 R MERGE FOR SHELL (I) : 0.99000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
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 (%): 54.66
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 1.26 M AMMONIUM
REMARK 280 SULFATE, 0.1 M TRIS PH 8.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 295K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4
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 -Y,X,Z
REMARK 290 4555 Y,-X,Z
REMARK 290 5555 X+1/2,Y+1/2,Z+1/2
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2
REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2
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 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 53.12500
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.12500
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.42500
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 53.12500
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.12500
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.42500
REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 53.12500
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 53.12500
REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 35.42500
REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 53.12500
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 53.12500
REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 35.42500
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 250 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 14410 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 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 ASN A 15 4.51 54.29
REMARK 500 ASP A 71 -71.32 -123.70
REMARK 500 ASP A 164 -46.52 76.66
REMARK 500 SER A 220 34.12 -91.63
REMARK 500 PRO A 245 34.21 -84.55
REMARK 500 ASN A 253 107.71 -55.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 CPS A 409
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 8VC A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 405
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 406
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CPS A 409
DBREF 5YIB A 4 331 UNP Q8I6V3 Q8I6V3_PLAF7 126 453
SEQRES 1 A 328 SER ASN ASP ASN ILE GLU LEU VAL ASP PHE GLN ASN ILE
SEQRES 2 A 328 MET PHE TYR GLY ASP ALA GLU VAL GLY ASP ASN GLN GLN
SEQRES 3 A 328 PRO PHE THR PHE ILE LEU ASP THR GLY SER ALA ASN LEU
SEQRES 4 A 328 TRP VAL PRO SER VAL LYS CYS THR THR ALA GLY CYS LEU
SEQRES 5 A 328 THR LYS HIS LEU TYR ASP SER SER LYS SER ARG THR TYR
SEQRES 6 A 328 GLU LYS ASP GLY THR LYS VAL GLU MET ASN TYR VAL SER
SEQRES 7 A 328 GLY THR VAL SER GLY PHE PHE SER LYS ASP LEU VAL THR
SEQRES 8 A 328 VAL GLY ASN LEU SER LEU PRO TYR LYS PHE ILE GLU VAL
SEQRES 9 A 328 ILE ASP THR ASN GLY PHE GLU PRO THR TYR THR ALA SER
SEQRES 10 A 328 THR PHE ASP GLY ILE LEU GLY LEU GLY TRP LYS ASP LEU
SEQRES 11 A 328 SER ILE GLY SER VAL ASP PRO ILE VAL VAL GLU LEU LYS
SEQRES 12 A 328 ASN GLN ASN LYS ILE GLU ASN ALA LEU PHE THR PHE TYR
SEQRES 13 A 328 LEU PRO VAL HIS ASP LYS HIS THR GLY PHE LEU THR ILE
SEQRES 14 A 328 GLY GLY ILE GLU GLU ARG PHE TYR GLU GLY PRO LEU THR
SEQRES 15 A 328 TYR GLU LYS LEU ASN HIS ASP LEU TYR TRP GLN ILE THR
SEQRES 16 A 328 LEU ASP ALA HIS VAL GLY ASN ILE MET LEU GLU LYS ALA
SEQRES 17 A 328 ASN CYS ILE VAL ASP SER GLY THR SER ALA ILE THR VAL
SEQRES 18 A 328 PRO THR ASP PHE LEU ASN LYS MET LEU GLN ASN LEU ASP
SEQRES 19 A 328 VAL ILE LYS VAL PRO PHE LEU PRO PHE TYR VAL THR LEU
SEQRES 20 A 328 CYS ASN ASN SER LYS LEU PRO THR PHE GLU PHE THR SER
SEQRES 21 A 328 GLU ASN GLY LYS TYR THR LEU GLU PRO GLU TYR TYR LEU
SEQRES 22 A 328 GLN HIS ILE GLU ASP VAL GLY PRO GLY LEU CYS MET LEU
SEQRES 23 A 328 ASN ILE ILE GLY LEU ASP PHE PRO VAL PRO THR PHE ILE
SEQRES 24 A 328 LEU GLY ASP PRO PHE MET ARG LYS TYR PHE THR VAL PHE
SEQRES 25 A 328 ASP TYR ASP ASN GLN SER VAL GLY ILE ALA LEU ALA LYS
SEQRES 26 A 328 LYS ASN LEU
HET 8VC A 401 52
HET GOL A 402 6
HET GOL A 403 6
HET GOL A 404 6
HET GOL A 405 6
HET GOL A 406 6
HET EDO A 407 4
HET EDO A 408 4
HET CPS A 409 31
HETNAM 8VC (4R)-3-[(2S,3S)-3-[2-[4-[2-(DIMETHYLAMINO)ETHYL-METHYL-
HETNAM 2 8VC AMINO]-2,6-DIMETHYL-PHENOXY]ETHANOYLAMINO]-2-OXIDANYL-
HETNAM 3 8VC 4-PHENYL-BUTANOYL]-5,5-DIMETHYL-N-[(1S,2R)-2-OXIDANYL-
HETNAM 4 8VC 2,3-DIHYDRO-1H-INDEN-1-YL]-1,3-THIAZOLIDINE-4-
HETNAM 5 8VC CARBOXAMIDE
HETNAM GOL GLYCEROL
HETNAM EDO 1,2-ETHANEDIOL
HETNAM CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-
HETNAM 2 CPS PROPANESULFONATE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
HETSYN EDO ETHYLENE GLYCOL
HETSYN CPS CHAPS
FORMUL 2 8VC C40 H53 N5 O6 S
FORMUL 3 GOL 5(C3 H8 O3)
FORMUL 8 EDO 2(C2 H6 O2)
FORMUL 10 CPS C32 H58 N2 O7 S
FORMUL 11 HOH *114(H2 O)
HELIX 1 AA1 THR A 51 LYS A 57 5 7
HELIX 2 AA2 ASP A 61 SER A 65 5 5
HELIX 3 AA3 THR A 110 GLU A 114 5 5
HELIX 4 AA4 PRO A 115 SER A 120 1 6
HELIX 5 AA5 TRP A 130 SER A 134 5 5
HELIX 6 AA6 PRO A 140 GLN A 148 1 9
HELIX 7 AA7 GLU A 176 ARG A 178 5 3
HELIX 8 AA8 PRO A 225 GLN A 234 1 10
HELIX 9 AA9 GLU A 271 TYR A 275 1 5
HELIX 10 AB1 GLY A 304 LYS A 310 1 7
SHEET 1 AA1 9 GLU A 69 TYR A 79 0
SHEET 2 AA1 9 GLY A 82 VAL A 95 -1 O VAL A 84 N MET A 77
SHEET 3 AA1 9 MET A 17 VAL A 24 -1 N GLU A 23 O THR A 94
SHEET 4 AA1 9 ASP A 6 PHE A 13 -1 N PHE A 13 O MET A 17
SHEET 5 AA1 9 GLY A 168 ILE A 172 -1 O ILE A 172 N ASP A 6
SHEET 6 AA1 9 LEU A 155 TYR A 159 -1 N TYR A 159 O PHE A 169
SHEET 7 AA1 9 TYR A 311 ASP A 316 -1 O PHE A 315 N PHE A 156
SHEET 8 AA1 9 SER A 321 ALA A 327 -1 O GLY A 323 N VAL A 314
SHEET 9 AA1 9 TYR A 180 LYS A 188 -1 N THR A 185 O ILE A 324
SHEET 1 AA213 GLU A 69 TYR A 79 0
SHEET 2 AA213 GLY A 82 VAL A 95 -1 O VAL A 84 N MET A 77
SHEET 3 AA213 LEU A 98 ASP A 109 -1 O GLU A 106 N PHE A 87
SHEET 4 AA213 LEU A 42 PRO A 45 1 N VAL A 44 O VAL A 107
SHEET 5 AA213 GLY A 124 GLY A 127 -1 O ILE A 125 N TRP A 43
SHEET 6 AA213 GLN A 29 ASP A 36 1 N ILE A 34 O LEU A 126
SHEET 7 AA213 MET A 17 VAL A 24 -1 N GLY A 20 O PHE A 33
SHEET 8 AA213 ASP A 6 PHE A 13 -1 N PHE A 13 O MET A 17
SHEET 9 AA213 GLY A 168 ILE A 172 -1 O ILE A 172 N ASP A 6
SHEET 10 AA213 LEU A 155 TYR A 159 -1 N TYR A 159 O PHE A 169
SHEET 11 AA213 TYR A 311 ASP A 316 -1 O PHE A 315 N PHE A 156
SHEET 12 AA213 SER A 321 ALA A 327 -1 O GLY A 323 N VAL A 314
SHEET 13 AA213 TYR A 180 LYS A 188 -1 N THR A 185 O ILE A 324
SHEET 1 AA3 7 LYS A 267 LEU A 270 0
SHEET 2 AA3 7 PHE A 259 THR A 262 -1 N PHE A 261 O TYR A 268
SHEET 3 AA3 7 GLN A 196 VAL A 203 -1 N HIS A 202 O GLU A 260
SHEET 4 AA3 7 ILE A 206 VAL A 215 -1 O LEU A 208 N ALA A 201
SHEET 5 AA3 7 THR A 300 LEU A 303 1 O LEU A 303 N ILE A 214
SHEET 6 AA3 7 ILE A 222 VAL A 224 -1 N THR A 223 O ILE A 302
SHEET 7 AA3 7 ILE A 291 GLY A 293 1 O ILE A 292 N VAL A 224
SHEET 1 AA4 4 ILE A 239 LYS A 240 0
SHEET 2 AA4 4 TYR A 247 LEU A 250 -1 O VAL A 248 N ILE A 239
SHEET 3 AA4 4 LEU A 286 LEU A 289 -1 O CYS A 287 N THR A 249
SHEET 4 AA4 4 LEU A 276 HIS A 278 -1 N GLN A 277 O MET A 288
SSBOND 1 CYS A 49 CYS A 54 1555 1555 2.06
SSBOND 2 CYS A 251 CYS A 287 1555 1555 2.09
CISPEP 1 GLU A 114 PRO A 115 0 5.97
SITE 1 AC1 18 ILE A 34 ASP A 36 GLY A 38 MET A 77
SITE 2 AC1 18 TYR A 79 VAL A 80 SER A 81 LEU A 133
SITE 3 AC1 18 SER A 134 ASP A 216 GLY A 218 THR A 219
SITE 4 AC1 18 SER A 220 ILE A 292 PHE A 296 ILE A 302
SITE 5 AC1 18 EDO A 407 CPS A 409
SITE 1 AC2 3 GLU A 181 GLY A 182 LYS A 328
SITE 1 AC3 3 SER A 220 MET A 288 ASN A 290
SITE 1 AC4 3 LYS A 48 TYR A 68 LYS A 70
SITE 1 AC5 7 ASN A 235 LEU A 236 ASP A 237 VAL A 238
SITE 2 AC5 7 LYS A 240 HOH A 503 HOH A 529
SITE 1 AC6 4 THR A 198 ASP A 200 SER A 263 GLU A 264
SITE 1 AC7 5 GLY A 38 TYR A 194 ILE A 214 8VC A 401
SITE 2 AC7 5 HOH A 549
SITE 1 AC8 3 THR A 269 LYS A 310 HOH A 557
SITE 1 AC9 8 VAL A 80 SER A 81 THR A 116 SER A 254
SITE 2 AC9 8 LYS A 255 LEU A 294 8VC A 401 HOH A 587
CRYST1 106.250 106.250 70.850 90.00 90.00 90.00 I 4 8
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 0.009412 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009412 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014114 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
