HEADER HYDROLASE 15-MAY-18 5QGN
TITLE PANDDA ANALYSIS GROUP DEPOSITION OF MODELS WITH MODELLED EVENTS (E.G.
TITLE 2 BOUND LIGANDS) -- CRYSTAL STRUCTURE OF NUDT7 IN COMPLEX WITH OX-210
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PEROXISOMAL COENZYME A DIPHOSPHATASE NUDT7;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 7,NUDIX MOTIF
COMPND 5 7;
COMPND 6 EC: 3.6.1.-;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: NUDT7;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS PANDDA, SGC - DIAMOND I04-1 FRAGMENT SCREENING, NUDIX DOMAIN,
KEYWDS 2 XCHEMEXPLORER, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR T.KROJER,R.TALON,M.FAIRHEAD,L.DIAZ SAEZ,A.R.BRADLEY,A.AIMON,
AUTHOR 2 P.COLLINS,J.BRANDAO-NETO,A.DOUANGAMATH,G.F.RUDA,T.SZOMMER,
AUTHOR 3 V.SRIKANNATHASAN,J.ELKINS,J.SPENCER,N.LONDON,A.NELSON,P.E.BRENNAN,
AUTHOR 4 K.HUBER,C.BOUNTRA,C.H.ARROWSMITH,A.EDWARDS,F.VON DELFT
REVDAT 2 15-NOV-23 5QGN 1 REMARK
REVDAT 1 27-MAR-19 5QGN 0
JRNL AUTH T.KROJER,R.TALON,M.FAIRHEAD,L.DIAZ SAEZ,A.R.BRADLEY,A.AIMON,
JRNL AUTH 2 P.COLLINS,J.BRANDAO-NETO,A.DOUANGAMATH,G.F.RUDA,T.SZOMMER,
JRNL AUTH 3 V.SRIKANNATHASAN,J.ELKINS,J.SPENCER,N.LONDON,A.NELSON,
JRNL AUTH 4 P.E.BRENNAN,K.HUBER,C.BOUNTRA,C.H.ARROWSMITH,A.EDWARDS,
JRNL AUTH 5 F.VON DELFT
JRNL TITL PANDDA ANALYSIS GROUP DEPOSITION OF MODELS WITH MODELLED
JRNL TITL 2 EVENTS (E.G. BOUND LIGANDS)
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.95 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0189
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 109.27
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7
REMARK 3 NUMBER OF REFLECTIONS : 26341
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) : 0.192
REMARK 3 R VALUE (WORKING SET) : 0.191
REMARK 3 FREE R VALUE : 0.211
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 1355
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) : 1.95
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1902
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.60
REMARK 3 BIN R VALUE (WORKING SET) : 0.2740
REMARK 3 BIN FREE R VALUE SET COUNT : 75
REMARK 3 BIN FREE R VALUE : 0.2790
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1467
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 58
REMARK 3 SOLVENT ATOMS : 166
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.31
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.18000
REMARK 3 B22 (A**2) : 0.18000
REMARK 3 B33 (A**2) : -0.60000
REMARK 3 B12 (A**2) : 0.09000
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): 0.112
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.748
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1557 ; 0.015 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 1459 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2113 ; 1.699 ; 1.994
REMARK 3 BOND ANGLES OTHERS (DEGREES): 3380 ; 0.984 ; 2.984
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 184 ; 5.990 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 66 ;34.262 ;24.242
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 252 ;15.029 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;19.886 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 237 ; 0.111 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1722 ; 0.008 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 298 ; 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): 744 ; 2.825 ; 3.267
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 741 ; 2.745 ; 3.253
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 924 ; 3.865 ; 4.846
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
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 : MASK
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 U VALUES : REFINED INDIVIDUALLY
REMARK 4
REMARK 4 5QGN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-18.
REMARK 100 THE DEPOSITION ID IS D_1001401924.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 11-MAY-17
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I04-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28045
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950
REMARK 200 RESOLUTION RANGE LOW (A) : 29.330
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 10.10
REMARK 200 R MERGE (I) : 0.06100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0
REMARK 200 DATA REDUNDANCY IN SHELL : 10.20
REMARK 200 R MERGE FOR SHELL (I) : 0.70700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS
REMARK 200 SOFTWARE USED: REFMAC
REMARK 200 STARTING MODEL: 5T3P
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 71.48
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.31
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 5.5 -- 0.1M AMMONIUM
REMARK 280 ACETATE -- 5%(W/V) PEG10K, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z
REMARK 290 3555 -X+Y,-X,Z
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z
REMARK 290 6555 -X,-X+Y,-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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 760 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 10430 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 5.0 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 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 HIS A 162
REMARK 465 TYR A 163
REMARK 465 VAL A 164
REMARK 465 THR A 165
REMARK 465 ARG A 166
REMARK 465 LEU A 167
REMARK 465 GLY A 168
REMARK 465 HIS A 169
REMARK 465 ARG A 170
REMARK 465 PHE A 171
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLN A 161 CG CD OE1 NE2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O GLN A 136 O HOH A 401 2.00
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 448 O HOH A 448 6559 1.38
REMARK 500
REMARK 500 REMARK: NULL
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 92 NE - CZ - NH1 ANGL. DEV. = 3.7 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 THR A 118 -21.34 70.96
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue H4D A 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue H4D A 306
DBREF 5QGN A 15 210 UNP P0C024 NUDT7_HUMAN 14 209
SEQADV 5QGN MET A 16 UNP P0C024 LEU 15 CONFLICT
SEQRES 1 A 196 SER MET LEU ASP ASP ALA LYS ALA ARG LEU ARG LYS TYR
SEQRES 2 A 196 ASP ILE GLY GLY LYS TYR SER HIS LEU PRO TYR ASN LYS
SEQRES 3 A 196 TYR SER VAL LEU LEU PRO LEU VAL ALA LYS GLU GLY LYS
SEQRES 4 A 196 LEU HIS LEU LEU PHE THR VAL ARG SER GLU LYS LEU ARG
SEQRES 5 A 196 ARG ALA PRO GLY GLU VAL CYS PHE PRO GLY GLY LYS ARG
SEQRES 6 A 196 ASP PRO THR ASP MET ASP ASP ALA ALA THR ALA LEU ARG
SEQRES 7 A 196 GLU ALA GLN GLU GLU VAL GLY LEU ARG HYP HIS GLN VAL
SEQRES 8 A 196 GLU VAL VAL CSO CYS LEU VAL PRO CYS LEU ILE ASP THR
SEQRES 9 A 196 ASP THR LEU ILE THR PRO PHE VAL GLY LEU ILE ASP HIS
SEQRES 10 A 196 ASN PHE GLN ALA GLN PRO ASN PRO ALA GLU VAL LYS ASP
SEQRES 11 A 196 VAL PHE LEU VAL PRO LEU ALA TYR PHE LEU HIS PRO GLN
SEQRES 12 A 196 VAL HIS ASP GLN HIS TYR VAL THR ARG LEU GLY HIS ARG
SEQRES 13 A 196 PHE ILE ASN HIS ILE PHE GLU TYR THR ASN PRO GLU ASP
SEQRES 14 A 196 GLY VAL THR TYR GLN ILE LYS GLY MET THR ALA ASN LEU
SEQRES 15 A 196 ALA VAL LEU VAL ALA PHE ILE ILE LEU GLU LYS LYS PRO
SEQRES 16 A 196 THR
MODRES 5QGN HYP A 102 PRO MODIFIED RESIDUE
MODRES 5QGN CSO A 109 CYS MODIFIED RESIDUE
HET HYP A 102 8
HET CSO A 109 7
HET ACT A 301 4
HET ACT A 302 4
HET DMS A 303 4
HET DMS A 304 4
HET H4D A 305 21
HET H4D A 306 21
HETNAM HYP 4-HYDROXYPROLINE
HETNAM CSO S-HYDROXYCYSTEINE
HETNAM ACT ACETATE ION
HETNAM DMS DIMETHYL SULFOXIDE
HETNAM H4D 3-BORONO-5-{[(THIOPHEN-2-YL)ACETYL]AMINO}BENZOIC ACID
HETSYN HYP HYDROXYPROLINE
FORMUL 1 HYP C5 H9 N O3
FORMUL 1 CSO C3 H7 N O3 S
FORMUL 2 ACT 2(C2 H3 O2 1-)
FORMUL 4 DMS 2(C2 H6 O S)
FORMUL 6 H4D 2(C13 H12 B N O5 S)
FORMUL 8 HOH *166(H2 O)
HELIX 1 AA1 SER A 15 LYS A 26 1 12
HELIX 2 AA2 ASP A 85 GLY A 99 1 15
HELIX 3 AA3 ARG A 101 HIS A 103 5 3
HELIX 4 AA4 ALA A 151 HIS A 155 5 5
HELIX 5 AA5 LYS A 190 GLU A 206 1 17
SHEET 1 AA1 4 VAL A 105 CYS A 110 0
SHEET 2 AA1 4 THR A 120 ILE A 129 -1 O VAL A 126 N VAL A 108
SHEET 3 AA1 4 ASN A 39 LYS A 50 1 N LEU A 47 O GLY A 127
SHEET 4 AA1 4 LYS A 53 ARG A 61 -1 O LYS A 53 N LYS A 50
SHEET 1 AA2 4 CYS A 114 ILE A 116 0
SHEET 2 AA2 4 THR A 120 ILE A 129 -1 O ILE A 122 N CYS A 114
SHEET 3 AA2 4 ASN A 39 LYS A 50 1 N LEU A 47 O GLY A 127
SHEET 4 AA2 4 GLY A 76 LYS A 78 -1 O GLY A 77 N SER A 42
SHEET 1 AA3 3 VAL A 142 PRO A 149 0
SHEET 2 AA3 3 LYS A 53 ARG A 61 -1 N VAL A 60 O ASP A 144
SHEET 3 AA3 3 VAL A 72 CYS A 73 -1 O CYS A 73 N THR A 59
SHEET 1 AA4 3 VAL A 158 ASP A 160 0
SHEET 2 AA4 3 HIS A 174 THR A 179 -1 O ILE A 175 N HIS A 159
SHEET 3 AA4 3 THR A 186 ILE A 189 -1 O TYR A 187 N TYR A 178
LINK C ARG A 101 N HYP A 102 1555 1555 1.34
LINK C HYP A 102 N HIS A 103 1555 1555 1.33
LINK C VAL A 108 N CSO A 109 1555 1555 1.34
LINK C CSO A 109 N CYS A 110 1555 1555 1.31
SITE 1 AC1 5 GLY A 70 VAL A 72 TYR A 187 GLN A 188
SITE 2 AC1 5 HOH A 404
SITE 1 AC2 3 HYP A 102 HIS A 103 VAL A 105
SITE 1 AC3 6 GLY A 99 ARG A 101 GLN A 104 PHE A 133
SITE 2 AC3 6 GLN A 134 GLN A 136
SITE 1 AC4 4 ASP A 130 HIS A 131 ASP A 144 TYR A 187
SITE 1 AC5 10 THR A 59 ARG A 61 LEU A 65 ARG A 66
SITE 2 AC5 10 ARG A 67 CYS A 73 GLY A 76 GLU A 97
SITE 3 AC5 10 H4D A 306 HOH A 451
SITE 1 AC6 8 TYR A 41 VAL A 43 GLY A 77 LYS A 78
SITE 2 AC6 8 GLU A 93 H4D A 305 HOH A 423 HOH A 451
CRYST1 126.179 126.179 41.665 90.00 90.00 120.00 P 3 2 1 6
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 0.007925 0.004576 0.000000 0.00000
SCALE2 0.000000 0.009151 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024001 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
