HEADER HYDROLASE 14-MAY-08 3D4B
TITLE CRYSTAL STRUCTURE OF SIR2TM IN COMPLEX WITH ACETYL P53 PEPTIDE AND
TITLE 2 DADME-NAD+
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: NAD-DEPENDENT DEACETYLASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: REGULATORY PROTEIN SIR2 HOMOLOG;
COMPND 5 EC: 3.5.1.-;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: ACETYL P53 PEPTIDE;
COMPND 9 CHAIN: D;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA;
SOURCE 3 ORGANISM_TAXID: 2336;
SOURCE 4 GENE: NPDA, TM_0490;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL-21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A;
SOURCE 9 MOL_ID: 2;
SOURCE 10 SYNTHETIC: YES
KEYWDS ROSSMANN FOLD, CYTOPLASM, HYDROLASE, METAL-BINDING, NAD, ZINC
EXPDTA X-RAY DIFFRACTION
AUTHOR W.F.HAWSE,K.G.HOFF,D.FATKINS,A.DAINES,O.V.ZUBKOVA,V.L.SCHRAMM,
AUTHOR 2 W.ZHENG,C.WOLBERGER
REVDAT 3 16-OCT-24 3D4B 1 REMARK LINK
REVDAT 2 24-FEB-09 3D4B 1 VERSN
REVDAT 1 30-SEP-08 3D4B 0
JRNL AUTH W.F.HAWSE,K.G.HOFF,D.G.FATKINS,A.DAINES,O.V.ZUBKOVA,
JRNL AUTH 2 V.L.SCHRAMM,W.ZHENG,C.WOLBERGER
JRNL TITL STRUCTURAL INSIGHTS INTO INTERMEDIATE STEPS IN THE SIR2
JRNL TITL 2 DEACETYLATION REACTION.
JRNL REF STRUCTURE V. 16 1368 2008
JRNL REFN ISSN 0969-2126
JRNL PMID 18786399
JRNL DOI 10.1016/J.STR.2008.05.015
REMARK 2
REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0005
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) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 3 NUMBER OF REFLECTIONS : 22339
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) : 0.197
REMARK 3 R VALUE (WORKING SET) : 0.195
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 : 1170
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) : 1.90
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1578
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.54
REMARK 3 BIN R VALUE (WORKING SET) : 0.2570
REMARK 3 BIN FREE R VALUE SET COUNT : 69
REMARK 3 BIN FREE R VALUE : 0.3210
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1851
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 45
REMARK 3 SOLVENT ATOMS : 142
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.55
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.86000
REMARK 3 B22 (A**2) : 0.23000
REMARK 3 B33 (A**2) : -1.10000
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): 0.144
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.134
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.058
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1930 ; 0.016 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2619 ; 3.431 ; 2.018
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 237 ; 5.707 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 75 ;38.031 ;24.667
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 319 ;13.281 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;19.234 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 308 ; 0.111 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1413 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 888 ; 0.262 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1345 ; 0.333 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 142 ; 0.202 ; 0.200
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): 31 ; 0.154 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.125 ; 0.200
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): 1241 ; 1.148 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1935 ; 1.938 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 777 ; 2.857 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 684 ; 4.575 ; 4.500
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
REMARK 4
REMARK 4 3D4B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-08.
REMARK 100 THE DEPOSITION ID IS D_1000047574.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 03-JUL-05
REMARK 200 TEMPERATURE (KELVIN) : 77.4
REMARK 200 PH : 9.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 24-ID-C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : 0.99
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23509
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 200 DATA REDUNDANCY : 3.200
REMARK 200 R MERGE (I) : 0.10000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.37000
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: NULL
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.37
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, PH 9.5, VAPOR DIFFUSION,
REMARK 280 HANGING DROP, TEMPERATURE 292K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
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 22.89500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.05700
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.86750
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.05700
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.89500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.86750
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: 1310 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 10370 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D
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 ARG A 34
REMARK 465 GLY A 35
REMARK 465 PRO A 36
REMARK 465 ASN A 37
REMARK 465 GLY A 38
REMARK 465 ILE A 39
REMARK 465 TYR A 40
REMARK 465 LYS A 41
REMARK 465 LYS A 42
REMARK 465 TYR A 43
REMARK 465 SER A 44
REMARK 465 GLN A 45
REMARK 465 SER A 246
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 LYS A 4 CG CD CE NZ
REMARK 470 GLU A 5 CG CD OE1 OE2
REMARK 470 ARG A 14 CG CD NE CZ NH1 NH2
REMARK 470 GLU A 66 CG CD OE1 OE2
REMARK 470 GLU A 88 CG CD OE1 OE2
REMARK 470 LYS A 110 CD CE NZ
REMARK 470 LYS A 111 CG CD CE NZ
REMARK 470 ARG A 126 CD NE CZ NH1 NH2
REMARK 470 LYS A 138 CG CD CE NZ
REMARK 470 ASP A 144 CG OD1 OD2
REMARK 470 GLN A 168 CG CD OE1 NE2
REMARK 470 ARG A 172 CG CD NE CZ NH1 NH2
REMARK 470 ARG A 180 CD NE CZ NH1 NH2
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 HOH A 1086 O HOH A 1120 1.93
REMARK 500 O HOH A 1066 O HOH A 1090 2.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 PHE A 220 CG PHE A 220 CD1 -0.098
REMARK 500 PHE A 220 CD1 PHE A 220 CE1 -0.125
REMARK 500 LYS D 10 C ALY D 11 N 0.142
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 HIS A 56 58.86 -141.89
REMARK 500 ILE A 68 -57.00 -120.13
REMARK 500 MET A 71 -10.27 -49.46
REMARK 500 ARG A 102 18.62 55.08
REMARK 500 SER D 7 32.08 73.77
REMARK 500 ARG D 8 37.27 73.20
REMARK 500 HIS D 9 73.27 65.84
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 ZN A1001 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 124 SG
REMARK 620 2 CYS A 127 SG 113.5
REMARK 620 3 CYS A 148 SG 102.5 109.6
REMARK 620 4 CYS A 151 SG 95.3 118.2 115.9
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DZD A 1002
DBREF 3D4B A 1 246 UNP Q9WYW0 NPD_THEMA 1 246
DBREF 3D4B D 6 14 PDB 3D4B 3D4B 6 14
SEQRES 1 A 246 MET LYS MET LYS GLU PHE LEU ASP LEU LEU ASN GLU SER
SEQRES 2 A 246 ARG LEU THR VAL THR LEU THR GLY ALA GLY ILE SER THR
SEQRES 3 A 246 PRO SER GLY ILE PRO ASP PHE ARG GLY PRO ASN GLY ILE
SEQRES 4 A 246 TYR LYS LYS TYR SER GLN ASN VAL PHE ASP ILE ASP PHE
SEQRES 5 A 246 PHE TYR SER HIS PRO GLU GLU PHE TYR ARG PHE ALA LYS
SEQRES 6 A 246 GLU GLY ILE PHE PRO MET LEU GLN ALA LYS PRO ASN LEU
SEQRES 7 A 246 ALA HIS VAL LEU LEU ALA LYS LEU GLU GLU LYS GLY LEU
SEQRES 8 A 246 ILE GLU ALA VAL ILE THR GLN ASN ILE ASP ARG LEU HIS
SEQRES 9 A 246 GLN ARG ALA GLY SER LYS LYS VAL ILE GLU LEU HIS GLY
SEQRES 10 A 246 ASN VAL GLU GLU TYR TYR CYS VAL ARG CYS GLU LYS LYS
SEQRES 11 A 246 TYR THR VAL GLU ASP VAL ILE LYS LYS LEU GLU SER SER
SEQRES 12 A 246 ASP VAL PRO LEU CYS ASP ASP CYS ASN SER LEU ILE ARG
SEQRES 13 A 246 PRO ASN ILE VAL PHE PHE GLY GLU ASN LEU PRO GLN ASP
SEQRES 14 A 246 ALA LEU ARG GLU ALA ILE GLY LEU SER SER ARG ALA SER
SEQRES 15 A 246 LEU MET ILE VAL LEU GLY SER SER LEU VAL VAL TYR PRO
SEQRES 16 A 246 ALA ALA GLU LEU PRO LEU ILE THR VAL ARG SER GLY GLY
SEQRES 17 A 246 LYS LEU VAL ILE VAL ASN LEU GLY GLU THR PRO PHE ASP
SEQRES 18 A 246 ASP ILE ALA THR LEU LYS TYR ASN MET ASP VAL VAL GLU
SEQRES 19 A 246 PHE ALA ARG ARG VAL MET GLU GLU GLY GLY ILE SER
SEQRES 1 D 9 THR SER ARG HIS LYS ALY LEU MET ALA
MODRES 3D4B ALY D 11 LYS N(6)-ACETYLLYSINE
HET ALY D 11 12
HET ZN A1001 1
HET DZD A1002 44
HETNAM ALY N(6)-ACETYLLYSINE
HETNAM ZN ZINC ION
HETNAM DZD 5'-O-[(R)-{[(R)-{[(3R,4R)-1-(3-CARBAMOYLBENZYL)-4-
HETNAM 2 DZD HYDROXYPYRROLIDIN-3-YL]METHOXY}(HYDROXY)
HETNAM 3 DZD PHOSPHORYL]METHYL}(HYDROXY)PHOSPHORYL]ADENOSINE
FORMUL 2 ALY C8 H16 N2 O3
FORMUL 3 ZN ZN 2+
FORMUL 4 DZD C24 H33 N7 O11 P2
FORMUL 5 HOH *142(H2 O)
HELIX 1 1 LYS A 2 SER A 13 1 12
HELIX 2 2 ALA A 22 GLY A 29 5 8
HELIX 3 3 ASP A 49 HIS A 56 1 8
HELIX 4 4 HIS A 56 ILE A 68 1 13
HELIX 5 5 PHE A 69 GLN A 73 5 5
HELIX 6 6 ASN A 77 LYS A 89 1 13
HELIX 7 7 ARG A 102 ALA A 107 1 6
HELIX 8 8 VAL A 133 LEU A 140 1 8
HELIX 9 9 PRO A 167 ALA A 181 1 15
HELIX 10 10 PRO A 195 ALA A 197 5 3
HELIX 11 11 GLU A 198 SER A 206 1 9
HELIX 12 12 PHE A 220 ALA A 224 5 5
HELIX 13 13 ASP A 231 GLY A 244 1 14
SHEET 1 A 6 VAL A 112 GLU A 114 0
SHEET 2 A 6 ALA A 94 THR A 97 1 N VAL A 95 O ILE A 113
SHEET 3 A 6 THR A 16 THR A 20 1 N THR A 18 O ILE A 96
SHEET 4 A 6 LEU A 183 LEU A 187 1 O ILE A 185 N LEU A 19
SHEET 5 A 6 LYS A 209 VAL A 213 1 O VAL A 211 N VAL A 186
SHEET 6 A 6 LEU A 226 TYR A 228 1 O TYR A 228 N ILE A 212
SHEET 1 B 3 LYS A 130 THR A 132 0
SHEET 2 B 3 GLY A 117 CYS A 124 -1 N TYR A 122 O TYR A 131
SHEET 3 B 3 ILE A 155 ILE A 159 -1 O ASN A 158 N GLU A 121
SHEET 1 C 2 VAL A 193 TYR A 194 0
SHEET 2 C 2 LEU D 12 MET D 13 -1 O LEU D 12 N TYR A 194
LINK C LYS D 10 N ALY D 11 1555 1555 1.48
LINK C ALY D 11 N LEU D 12 1555 1555 1.45
LINK SG CYS A 124 ZN ZN A1001 1555 1555 2.41
LINK SG CYS A 127 ZN ZN A1001 1555 1555 2.17
LINK SG CYS A 148 ZN ZN A1001 1555 1555 2.30
LINK SG CYS A 151 ZN ZN A1001 1555 1555 2.35
CISPEP 1 TYR A 194 PRO A 195 0 -0.11
SITE 1 AC1 4 CYS A 124 CYS A 127 CYS A 148 CYS A 151
SITE 1 AC2 28 GLY A 21 ALA A 22 GLY A 23 SER A 25
SITE 2 AC2 28 THR A 26 PRO A 27 ILE A 30 PRO A 31
SITE 3 AC2 28 ASP A 32 PHE A 33 GLN A 98 ASN A 99
SITE 4 AC2 28 ILE A 100 ASP A 101 HIS A 116 PHE A 162
SITE 5 AC2 28 GLY A 188 SER A 189 SER A 190 ASN A 214
SITE 6 AC2 28 LEU A 215 GLY A 216 MET A 230 ASP A 231
SITE 7 AC2 28 HOH A1003 HOH A1010 HOH A1077 HOH A1114
CRYST1 45.790 59.735 106.114 90.00 90.00 90.00 P 21 21 21 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 0.021839 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016741 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009424 0.00000