HEADER HYDROLASE 11-MAY-12 4F56 TITLE THE BICYCLIC INTERMEDIATE STRUCTURE PROVIDES INSIGHTS INTO THE TITLE 2 DESUCCINYLATION MECHANISM OF SIRT5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT LYSINE DEMALONYLASE AND DESUCCINYLASE COMPND 3 SIRTUIN-5, MITOCHONDRIAL; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: UNP RESIDUE 34-302; COMPND 6 SYNONYM: SIR2-LIKE PROTEIN 5; COMPND 7 EC: 3.5.1.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PEPTIDE FROM HISTONE H3.1; COMPND 11 CHAIN: C, D; COMPND 12 FRAGMENT: UNP RESIDUE 5-16; COMPND 13 SYNONYM: HISTONE H3/A, HISTONE H3/B, HISTONE H3/C, HISTONE H3/D, COMPND 14 HISTONE H3/F, HISTONE H3/H, HISTONE H3/I, HISTONE H3/J, HISTONE H3/K, COMPND 15 HISTONE H3/L; COMPND 16 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: SIR2L5, SIRT5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 R2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST-F1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS ZN-BINDING DOMAIN, ROSSMANN FOLD DOMAIN, NAD-DEPENDENT DEMALONYLASE KEYWDS 2 AND DESUCCINYLASE, MITOCHONDRIAL SIRTUIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHOU,Q.HAO REVDAT 4 08-NOV-23 4F56 1 REMARK SEQADV LINK REVDAT 3 15-NOV-17 4F56 1 REMARK REVDAT 2 19-SEP-12 4F56 1 JRNL REVDAT 1 20-JUN-12 4F56 0 JRNL AUTH Y.ZHOU,H.ZHANG,B.HE,J.DU,H.LIN,R.A.CERIONE,Q.HAO JRNL TITL THE BICYCLIC INTERMEDIATE STRUCTURE PROVIDES INSIGHTS INTO JRNL TITL 2 THE DESUCCINYLATION MECHANISM OF HUMAN SIRTUIN 5 (SIRT5) JRNL REF J.BIOL.CHEM. V. 287 28307 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22767592 JRNL DOI 10.1074/JBC.M112.384511 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 60314 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3053 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3787 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 187 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4222 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 408 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.68000 REMARK 3 B22 (A**2) : 0.29000 REMARK 3 B33 (A**2) : -0.98000 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): 0.170 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.480 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4503 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6146 ; 1.530 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 575 ; 5.721 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 193 ;34.979 ;22.591 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 698 ;13.952 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;18.737 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 669 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3451 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 4503 ; 3.037 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 127 ;26.889 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4658 ;11.873 ; 5.000 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 USED IF PRESENT IN REMARK 3 THE INPUT U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4F56 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000072468. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 REMARK 200 MONOCHROMATOR : HORIZONTAL BENT SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60804 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.45800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3RIY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 10000, 0.1M TRIS, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 26.20150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.43050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.37750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 78.43050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.20150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.37750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 REMARK 350 BIOMOLECULE: 2 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: 2010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 GLY A 30 REMARK 465 SER A 31 REMARK 465 PHE A 32 REMARK 465 THR A 33 REMARK 465 ALA A 34 REMARK 465 ARG A 35 REMARK 465 GLY B 30 REMARK 465 LYS C 4 REMARK 465 GLN C 5 REMARK 465 GLY C 13 REMARK 465 LYS C 14 REMARK 465 ALA C 15 REMARK 465 LYS D 4 REMARK 465 GLN D 5 REMARK 465 GLY D 13 REMARK 465 LYS D 14 REMARK 465 ALA D 15 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 ALA A 73 -119.39 46.89 REMARK 500 ARG A 78 -129.27 47.33 REMARK 500 ASN A 94 66.73 -156.80 REMARK 500 ARG B 78 -129.27 48.34 REMARK 500 ASN B 94 68.20 -155.01 REMARK 500 SER B 168 -65.16 -98.45 REMARK 500 CYS B 212 -83.34 -105.13 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 A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 166 SG REMARK 620 2 CYS A 169 SG 113.0 REMARK 620 3 CYS A 207 SG 106.9 110.9 REMARK 620 4 CYS A 212 SG 103.7 115.3 106.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 166 SG REMARK 620 2 CYS B 169 SG 105.7 REMARK 620 3 CYS B 207 SG 108.5 113.1 REMARK 620 4 CYS B 212 SG 100.8 114.7 112.8 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CGK C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CGK D 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F4U RELATED DB: PDB REMARK 900 RELATED ID: 3RIY RELATED DB: PDB REMARK 900 RELATED ID: 3RIG RELATED DB: PDB DBREF 4F56 A 34 302 UNP Q9NXA8 SIRT5_HUMAN 34 302 DBREF 4F56 B 34 302 UNP Q9NXA8 SIRT5_HUMAN 34 302 DBREF 4F56 C 4 15 UNP P68431 H31_HUMAN 5 16 DBREF 4F56 D 4 15 UNP P68431 H31_HUMAN 5 16 SEQADV 4F56 GLY A 30 UNP Q9NXA8 EXPRESSION TAG SEQADV 4F56 SER A 31 UNP Q9NXA8 EXPRESSION TAG SEQADV 4F56 PHE A 32 UNP Q9NXA8 EXPRESSION TAG SEQADV 4F56 THR A 33 UNP Q9NXA8 EXPRESSION TAG SEQADV 4F56 GLY B 30 UNP Q9NXA8 EXPRESSION TAG SEQADV 4F56 SER B 31 UNP Q9NXA8 EXPRESSION TAG SEQADV 4F56 PHE B 32 UNP Q9NXA8 EXPRESSION TAG SEQADV 4F56 THR B 33 UNP Q9NXA8 EXPRESSION TAG SEQRES 1 A 273 GLY SER PHE THR ALA ARG PRO SER SER SER MET ALA ASP SEQRES 2 A 273 PHE ARG LYS PHE PHE ALA LYS ALA LYS HIS ILE VAL ILE SEQRES 3 A 273 ILE SER GLY ALA GLY VAL SER ALA GLU SER GLY VAL PRO SEQRES 4 A 273 THR PHE ARG GLY ALA GLY GLY TYR TRP ARG LYS TRP GLN SEQRES 5 A 273 ALA GLN ASP LEU ALA THR PRO LEU ALA PHE ALA HIS ASN SEQRES 6 A 273 PRO SER ARG VAL TRP GLU PHE TYR HIS TYR ARG ARG GLU SEQRES 7 A 273 VAL MET GLY SER LYS GLU PRO ASN ALA GLY HIS ARG ALA SEQRES 8 A 273 ILE ALA GLU CYS GLU THR ARG LEU GLY LYS GLN GLY ARG SEQRES 9 A 273 ARG VAL VAL VAL ILE THR GLN ASN ILE ASP GLU LEU HIS SEQRES 10 A 273 ARG LYS ALA GLY THR LYS ASN LEU LEU GLU ILE HIS GLY SEQRES 11 A 273 SER LEU PHE LYS THR ARG CYS THR SER CYS GLY VAL VAL SEQRES 12 A 273 ALA GLU ASN TYR LYS SER PRO ILE CYS PRO ALA LEU SER SEQRES 13 A 273 GLY LYS GLY ALA PRO GLU PRO GLY THR GLN ASP ALA SER SEQRES 14 A 273 ILE PRO VAL GLU LYS LEU PRO ARG CYS GLU GLU ALA GLY SEQRES 15 A 273 CYS GLY GLY LEU LEU ARG PRO HIS VAL VAL TRP PHE GLY SEQRES 16 A 273 GLU ASN LEU ASP PRO ALA ILE LEU GLU GLU VAL ASP ARG SEQRES 17 A 273 GLU LEU ALA HIS CYS ASP LEU CYS LEU VAL VAL GLY THR SEQRES 18 A 273 SER SER VAL VAL TYR PRO ALA ALA MET PHE ALA PRO GLN SEQRES 19 A 273 VAL ALA ALA ARG GLY VAL PRO VAL ALA GLU PHE ASN THR SEQRES 20 A 273 GLU THR THR PRO ALA THR ASN ARG PHE ARG PHE HIS PHE SEQRES 21 A 273 GLN GLY PRO CYS GLY THR THR LEU PRO GLU ALA LEU ALA SEQRES 1 B 273 GLY SER PHE THR ALA ARG PRO SER SER SER MET ALA ASP SEQRES 2 B 273 PHE ARG LYS PHE PHE ALA LYS ALA LYS HIS ILE VAL ILE SEQRES 3 B 273 ILE SER GLY ALA GLY VAL SER ALA GLU SER GLY VAL PRO SEQRES 4 B 273 THR PHE ARG GLY ALA GLY GLY TYR TRP ARG LYS TRP GLN SEQRES 5 B 273 ALA GLN ASP LEU ALA THR PRO LEU ALA PHE ALA HIS ASN SEQRES 6 B 273 PRO SER ARG VAL TRP GLU PHE TYR HIS TYR ARG ARG GLU SEQRES 7 B 273 VAL MET GLY SER LYS GLU PRO ASN ALA GLY HIS ARG ALA SEQRES 8 B 273 ILE ALA GLU CYS GLU THR ARG LEU GLY LYS GLN GLY ARG SEQRES 9 B 273 ARG VAL VAL VAL ILE THR GLN ASN ILE ASP GLU LEU HIS SEQRES 10 B 273 ARG LYS ALA GLY THR LYS ASN LEU LEU GLU ILE HIS GLY SEQRES 11 B 273 SER LEU PHE LYS THR ARG CYS THR SER CYS GLY VAL VAL SEQRES 12 B 273 ALA GLU ASN TYR LYS SER PRO ILE CYS PRO ALA LEU SER SEQRES 13 B 273 GLY LYS GLY ALA PRO GLU PRO GLY THR GLN ASP ALA SER SEQRES 14 B 273 ILE PRO VAL GLU LYS LEU PRO ARG CYS GLU GLU ALA GLY SEQRES 15 B 273 CYS GLY GLY LEU LEU ARG PRO HIS VAL VAL TRP PHE GLY SEQRES 16 B 273 GLU ASN LEU ASP PRO ALA ILE LEU GLU GLU VAL ASP ARG SEQRES 17 B 273 GLU LEU ALA HIS CYS ASP LEU CYS LEU VAL VAL GLY THR SEQRES 18 B 273 SER SER VAL VAL TYR PRO ALA ALA MET PHE ALA PRO GLN SEQRES 19 B 273 VAL ALA ALA ARG GLY VAL PRO VAL ALA GLU PHE ASN THR SEQRES 20 B 273 GLU THR THR PRO ALA THR ASN ARG PHE ARG PHE HIS PHE SEQRES 21 B 273 GLN GLY PRO CYS GLY THR THR LEU PRO GLU ALA LEU ALA SEQRES 1 C 12 LYS GLN THR ALA ARG LYS SER THR GLY GLY LYS ALA SEQRES 1 D 12 LYS GLN THR ALA ARG LYS SER THR GLY GLY LYS ALA HET ZN A 401 1 HET ZN B 401 1 HET CGK C 101 42 HET CGK D 101 42 HETNAM ZN ZINC ION HETNAM CGK 3-[(2R,3AR,5R,6R,6AR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5- HETNAM 2 CGK (6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN- HETNAM 3 CGK 2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY) HETNAM 4 CGK PHOSPHORYL]OXY}METHYL)-2,6-DIHYDROXYTETRAHYDROFURO[2, HETNAM 5 CGK 3-D][1,3]OXATHIOL-2-YL]PROPANOIC ACID FORMUL 5 ZN 2(ZN 2+) FORMUL 7 CGK 2(C19 H27 N5 O16 P2 S) FORMUL 9 HOH *408(H2 O) HELIX 1 1 SER A 39 ALA A 50 1 12 HELIX 2 2 ALA A 59 GLY A 66 5 8 HELIX 3 3 GLN A 81 ALA A 86 1 6 HELIX 4 4 THR A 87 ASN A 94 1 8 HELIX 5 5 ASN A 94 SER A 111 1 18 HELIX 6 6 ASN A 115 GLN A 131 1 17 HELIX 7 7 GLU A 144 GLY A 150 1 7 HELIX 8 8 CYS A 181 SER A 185 5 5 HELIX 9 9 PRO A 200 LEU A 204 5 5 HELIX 10 10 ASP A 228 CYS A 242 1 15 HELIX 11 11 PRO A 256 ALA A 258 5 3 HELIX 12 12 MET A 259 ARG A 267 1 9 HELIX 13 13 ALA A 281 PHE A 285 5 5 HELIX 14 14 PRO A 292 ALA A 302 1 11 HELIX 15 15 SER B 39 ALA B 50 1 12 HELIX 16 16 ALA B 59 GLY B 66 5 8 HELIX 17 17 GLN B 81 ALA B 86 1 6 HELIX 18 18 THR B 87 ASN B 94 1 8 HELIX 19 19 ASN B 94 GLY B 110 1 17 HELIX 20 20 ASN B 115 LYS B 130 1 16 HELIX 21 21 GLU B 144 GLY B 150 1 7 HELIX 22 22 CYS B 181 SER B 185 5 5 HELIX 23 23 PRO B 200 LEU B 204 5 5 HELIX 24 24 ASP B 228 CYS B 242 1 15 HELIX 25 25 PRO B 256 ALA B 258 5 3 HELIX 26 26 MET B 259 ARG B 267 1 9 HELIX 27 27 ALA B 281 PHE B 285 5 5 HELIX 28 28 PRO B 292 LEU B 301 1 10 SHEET 1 A 6 LEU A 154 GLU A 156 0 SHEET 2 A 6 ARG A 134 THR A 139 1 N VAL A 137 O LEU A 155 SHEET 3 A 6 HIS A 52 SER A 57 1 N ILE A 55 O ILE A 138 SHEET 4 A 6 LEU A 244 VAL A 248 1 O VAL A 248 N ILE A 56 SHEET 5 A 6 VAL A 271 ASN A 275 1 O ALA A 272 N CYS A 245 SHEET 6 A 6 PHE A 287 GLN A 290 1 O PHE A 289 N GLU A 273 SHEET 1 B 3 VAL A 172 GLU A 174 0 SHEET 2 B 3 GLY A 159 CYS A 166 -1 N THR A 164 O ALA A 173 SHEET 3 B 3 LEU A 216 VAL A 220 -1 O ARG A 217 N ARG A 165 SHEET 1 C 6 LEU B 154 GLU B 156 0 SHEET 2 C 6 ARG B 134 THR B 139 1 N THR B 139 O LEU B 155 SHEET 3 C 6 HIS B 52 SER B 57 1 N ILE B 53 O ARG B 134 SHEET 4 C 6 LEU B 244 VAL B 248 1 O VAL B 248 N ILE B 56 SHEET 5 C 6 VAL B 271 ASN B 275 1 O ALA B 272 N CYS B 245 SHEET 6 C 6 PHE B 287 GLN B 290 1 O PHE B 289 N GLU B 273 SHEET 1 D 3 VAL B 172 GLU B 174 0 SHEET 2 D 3 GLY B 159 CYS B 166 -1 N THR B 164 O ALA B 173 SHEET 3 D 3 LEU B 216 VAL B 220 -1 O ARG B 217 N ARG B 165 LINK NZ LYS C 9 CX CGK C 101 1555 1555 1.46 LINK NZ LYS D 9 CX CGK D 101 1555 1555 1.45 LINK SG CYS A 166 ZN ZN A 401 1555 1555 2.27 LINK SG CYS A 169 ZN ZN A 401 1555 1555 2.35 LINK SG CYS A 207 ZN ZN A 401 1555 1555 2.39 LINK SG CYS A 212 ZN ZN A 401 1555 1555 2.40 LINK SG CYS B 166 ZN ZN B 401 1555 1555 2.35 LINK SG CYS B 169 ZN ZN B 401 1555 1555 2.25 LINK SG CYS B 207 ZN ZN B 401 1555 1555 2.33 LINK SG CYS B 212 ZN ZN B 401 1555 1555 2.39 CISPEP 1 ALA A 73 GLY A 74 0 2.62 CISPEP 2 SER A 178 PRO A 179 0 -0.83 CISPEP 3 TYR A 255 PRO A 256 0 0.07 CISPEP 4 SER B 178 PRO B 179 0 -0.96 CISPEP 5 TYR B 255 PRO B 256 0 2.47 CISPEP 6 THR C 11 GLY C 12 0 5.23 CISPEP 7 THR D 11 GLY D 12 0 -4.93 SITE 1 AC1 4 CYS A 166 CYS A 169 CYS A 207 CYS A 212 SITE 1 AC2 4 CYS B 166 CYS B 169 CYS B 207 CYS B 212 SITE 1 AC3 30 GLY A 58 ALA A 59 GLY A 60 ALA A 63 SITE 2 AC3 30 GLU A 64 THR A 69 PHE A 70 ARG A 71 SITE 3 AC3 30 TYR A 102 ARG A 105 GLN A 140 ILE A 142 SITE 4 AC3 30 HIS A 158 VAL A 220 PHE A 223 GLY A 249 SITE 5 AC3 30 THR A 250 SER A 251 VAL A 254 ASN A 275 SITE 6 AC3 30 THR A 276 GLU A 277 PRO A 292 CYS A 293 SITE 7 AC3 30 HOH A 511 HOH A 697 LYS C 9 HOH C 201 SITE 8 AC3 30 HOH C 202 HOH C 203 SITE 1 AC4 32 GLY B 58 ALA B 59 GLY B 60 ALA B 63 SITE 2 AC4 32 GLU B 64 THR B 69 PHE B 70 ARG B 71 SITE 3 AC4 32 TYR B 102 ARG B 105 GLN B 140 ILE B 142 SITE 4 AC4 32 HIS B 158 VAL B 220 PHE B 223 GLY B 249 SITE 5 AC4 32 THR B 250 SER B 251 VAL B 254 ASN B 275 SITE 6 AC4 32 THR B 276 GLU B 277 PRO B 292 CYS B 293 SITE 7 AC4 32 HOH B 596 HOH B 698 LYS D 9 HOH D 201 SITE 8 AC4 32 HOH D 202 HOH D 203 HOH D 205 HOH D 206 CRYST1 52.403 66.755 156.861 90.00 90.00 90.00 P 21 21 21 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 0.019083 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014980 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006375 0.00000