HEADER HYDROLASE/LIGASE 25-JUN-13 4BVG TITLE CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH NATIVE ALKYLIMIDATE TITLE 2 FORMED FROM ACETYL-LYSINE ACS2-PEPTIDE CRYSTALLIZED IN PRESENCE OF TITLE 3 THE INHIBITOR EX-527 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 116-399; COMPND 5 SYNONYM: SIRT3, HSIRT3, REGULATORY PROTEIN SIR2 HOMOLOG 3, SIR2-LIKE COMPND 6 PROTEIN 3; COMPND 7 EC: 3.5.1.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIAL; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: RESIDUES 638-647; COMPND 13 SYNONYM: ACETYL-LYSINE ACS2-PEPTIDE, ACETATE--COA LIGASE 2, ACETYL-C COMPND 14 ACECS2, ACYL-COA SYNTHETASE SHORT-CHAIN FAMILY MEMBER 1; COMPND 15 EC: 6.2.1.1; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PVFT3S; 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 HYDROLASE-LIGASE COMPLEX, NAD-DEPENDENT DEACETYLASE, NATIVE KEYWDS 2 INTERMEDIATE EXPDTA X-RAY DIFFRACTION AUTHOR G.T.T.NGUYEN,M.GERTZ,M.WEYAND,C.STEEGBORN REVDAT 5 16-OCT-24 4BVG 1 REMARK REVDAT 4 20-DEC-23 4BVG 1 REMARK LINK REVDAT 3 30-JAN-19 4BVG 1 COMPND JRNL REMARK HET REVDAT 3 2 1 HETNAM HETSYN FORMUL LINK REVDAT 3 3 1 SITE ATOM REVDAT 2 07-AUG-13 4BVG 1 JRNL REVDAT 1 17-JUL-13 4BVG 0 JRNL AUTH M.GERTZ,F.FISCHER,G.T.NGUYEN,M.LAKSHMINARASIMHAN, JRNL AUTH 2 M.SCHUTKOWSKI,M.WEYAND,C.STEEGBORN JRNL TITL EX-527 INHIBITS SIRTUINS BY EXPLOITING THEIR UNIQUE JRNL TITL 2 NAD+-DEPENDENT DEACETYLATION MECHANISM. JRNL REF PROC. NATL. ACAD. SCI. V. 110 E2772 2013 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 23840057 JRNL DOI 10.1073/PNAS.1303628110 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 12267 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 646 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 911 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2207 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 56 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.37000 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): 0.438 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.285 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.189 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.264 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2356 ; 0.015 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3188 ; 1.936 ; 2.025 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 279 ; 6.484 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 98 ;35.028 ;22.551 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 368 ;17.410 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;18.704 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 364 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1736 ; 0.009 ; 0.022 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): 1122 ; 3.395 ; 3.981 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1399 ; 5.349 ; 5.954 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1233 ; 4.031 ; 4.405 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. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U REMARK 3 VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4BVG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1290057457. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-12 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 : BESSY REMARK 200 BEAMLINE : 14.1 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 : SI(111) MONOCHROMATOR REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12915 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 38.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 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: PDB ENTRY 3GLT REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M (NH4)2SO4, 0.1M BISTRIS PH 5.5, REMARK 280 21% PEG 3350, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 38.25400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.25400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 39.01150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.66450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.01150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.66450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.25400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.01150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.66450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.25400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.01150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.66450 REMARK 290 SMTRY3 8 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: 4720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 116 REMARK 465 SER A 117 REMARK 465 SER A 118 REMARK 465 ASP A 119 REMARK 465 LYS A 120 REMARK 465 GLY A 121 REMARK 465 ASP A 395 REMARK 465 GLY A 396 REMARK 465 PRO A 397 REMARK 465 ASP A 398 REMARK 465 LYS A 399 REMARK 465 ARG B 4 REMARK 465 LEU B 5 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 2026 O HOH A 2045 2.19 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 LEU A 216 CA - CB - CG ANGL. DEV. = 14.2 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 ASP A 156 -155.52 -85.62 REMARK 500 LEU A 168 14.57 -164.08 REMARK 500 GLN A 169 131.82 -37.32 REMARK 500 PRO A 201 118.09 -30.81 REMARK 500 GLN A 260 14.98 58.00 REMARK 500 ASP A 267 0.25 -61.75 REMARK 500 THR A 284 -3.08 73.19 REMARK 500 PRO A 289 152.08 -48.19 REMARK 500 ASP A 290 48.09 -76.94 REMARK 500 HIS A 354 79.28 -154.11 REMARK 500 GLN A 388 -76.35 -30.79 REMARK 500 ARG A 389 -5.62 -52.88 REMARK 500 GLU A 390 -79.66 -107.50 REMARK 500 LYS A 393 35.13 -77.20 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 A1409 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 256 SG REMARK 620 2 CYS A 259 SG 101.4 REMARK 620 3 CYS A 280 SG 106.5 106.0 REMARK 620 4 CYS A 283 SG 96.9 122.0 120.4 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 OAD B 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1396 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1397 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1398 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1399 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1403 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1404 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1405 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1406 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1407 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 1408 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BV2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH EX-527 AND 2'-O-ACETYL- REMARK 900 ADP-RIBOSE REMARK 900 RELATED ID: 4BV3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SIRT3 IN COMPLEX WITH EX-527 AND NAD REMARK 900 RELATED ID: 4BVB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH EX- 527 AND ADP- REMARK 900 RIBOSE REMARK 900 RELATED ID: 4BVE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE REMARK 900 FORMED FROM THIO-ACETYL-LYSINE ACS2- PEPTIDE REMARK 900 RELATED ID: 4BVF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE REMARK 900 FORMED FROM THIO-ACETYL-LYSINE ACS2- PEPTIDE CRYSTALLIZED IN REMARK 900 PRESENCE OF THE INHIBITOR EX- 527 REMARK 900 RELATED ID: 4BVH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX- REMARK 900 527 AND 2'-O-ACETYL-ADP-RIBOSE REMARK 900 RELATED ID: 4BUZ RELATED DB: PDB REMARK 900 SIR2 COMPLEX STRUCTURE MIXTURE OF EX-527 INHIBITOR AND REACTION REMARK 900 PRODUCTS OR OF REACTION SUBSTRATES P53 PEPTIDE AND NAD DBREF 4BVG A 116 399 UNP Q9NTG7 SIR3_HUMAN 116 399 DBREF 4BVG B -4 5 UNP Q9NUB1 ACS2L_HUMAN 638 647 SEQRES 1 A 284 GLY SER SER ASP LYS GLY LYS LEU SER LEU GLN ASP VAL SEQRES 2 A 284 ALA GLU LEU ILE ARG ALA ARG ALA CYS GLN ARG VAL VAL SEQRES 3 A 284 VAL MET VAL GLY ALA GLY ILE SER THR PRO SER GLY ILE SEQRES 4 A 284 PRO ASP PHE ARG SER PRO GLY SER GLY LEU TYR SER ASN SEQRES 5 A 284 LEU GLN GLN TYR ASP LEU PRO TYR PRO GLU ALA ILE PHE SEQRES 6 A 284 GLU LEU PRO PHE PHE PHE HIS ASN PRO LYS PRO PHE PHE SEQRES 7 A 284 THR LEU ALA LYS GLU LEU TYR PRO GLY ASN TYR LYS PRO SEQRES 8 A 284 ASN VAL THR HIS TYR PHE LEU ARG LEU LEU HIS ASP LYS SEQRES 9 A 284 GLY LEU LEU LEU ARG LEU TYR THR GLN ASN ILE ASP GLY SEQRES 10 A 284 LEU GLU ARG VAL SER GLY ILE PRO ALA SER LYS LEU VAL SEQRES 11 A 284 GLU ALA HIS GLY THR PHE ALA SER ALA THR CYS THR VAL SEQRES 12 A 284 CYS GLN ARG PRO PHE PRO GLY GLU ASP ILE ARG ALA ASP SEQRES 13 A 284 VAL MET ALA ASP ARG VAL PRO ARG CYS PRO VAL CYS THR SEQRES 14 A 284 GLY VAL VAL LYS PRO ASP ILE VAL PHE PHE GLY GLU PRO SEQRES 15 A 284 LEU PRO GLN ARG PHE LEU LEU HIS VAL VAL ASP PHE PRO SEQRES 16 A 284 MET ALA ASP LEU LEU LEU ILE LEU GLY THR SER LEU GLU SEQRES 17 A 284 VAL GLU PRO PHE ALA SER LEU THR GLU ALA VAL ARG SER SEQRES 18 A 284 SER VAL PRO ARG LEU LEU ILE ASN ARG ASP LEU VAL GLY SEQRES 19 A 284 PRO LEU ALA TRP HIS PRO ARG SER ARG ASP VAL ALA GLN SEQRES 20 A 284 LEU GLY ASP VAL VAL HIS GLY VAL GLU SER LEU VAL GLU SEQRES 21 A 284 LEU LEU GLY TRP THR GLU GLU MET ARG ASP LEU VAL GLN SEQRES 22 A 284 ARG GLU THR GLY LYS LEU ASP GLY PRO ASP LYS SEQRES 1 B 10 THR ARG SER GLY LYS VAL MET ARG ARG LEU HET EDO A1396 4 HET EDO A1397 4 HET EDO A1398 4 HET EDO A1399 4 HET GOL A1400 6 HET GOL A1401 6 HET GOL A1402 6 HET EDO A1403 4 HET EDO A1404 4 HET SO4 A1405 5 HET SO4 A1406 5 HET EDO A1407 4 HET PEG A1408 7 HET ZN A1409 1 HET XYQ B1000 38 HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM ZN ZINC ION HETNAM XYQ (2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6- HETNAM 2 XYQ AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2- HETNAM 3 XYQ YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY) HETNAM 4 XYQ PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2- HETNAM 5 XYQ YL ACETATE HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN XYQ ACETYL-RIBOSYL-ADP FORMUL 3 EDO 7(C2 H6 O2) FORMUL 7 GOL 3(C3 H8 O3) FORMUL 12 SO4 2(O4 S 2-) FORMUL 15 PEG C4 H10 O3 FORMUL 16 ZN ZN 2+ FORMUL 17 XYQ C17 H25 N5 O15 P2 FORMUL 18 HOH *56(H2 O) HELIX 1 1 SER A 124 ALA A 134 1 11 HELIX 2 2 ALA A 146 GLY A 153 5 8 HELIX 3 3 TYR A 175 PHE A 180 5 6 HELIX 4 4 GLU A 181 ASN A 188 1 8 HELIX 5 5 PRO A 189 LEU A 199 1 11 HELIX 6 6 ASN A 207 LYS A 219 1 13 HELIX 7 7 GLY A 232 SER A 237 1 6 HELIX 8 8 PRO A 240 SER A 242 5 3 HELIX 9 9 ILE A 268 ALA A 274 1 7 HELIX 10 10 PRO A 299 LEU A 303 5 5 HELIX 11 11 LEU A 304 ALA A 312 1 9 HELIX 12 12 PHE A 327 VAL A 334 5 8 HELIX 13 13 GLY A 349 HIS A 354 1 6 HELIX 14 14 ASP A 365 LEU A 377 1 13 HELIX 15 15 TRP A 379 GLY A 392 1 14 SHEET 1 AA 6 LEU A 244 GLU A 246 0 SHEET 2 AA 6 LEU A 222 THR A 227 1 O LEU A 225 N VAL A 245 SHEET 3 AA 6 VAL A 140 VAL A 144 1 O VAL A 140 N LEU A 223 SHEET 4 AA 6 LEU A 314 LEU A 318 1 O LEU A 314 N VAL A 141 SHEET 5 AA 6 ARG A 340 ASN A 344 1 O LEU A 341 N ILE A 317 SHEET 6 AA 6 ASP A 359 LEU A 363 1 O VAL A 360 N LEU A 342 SHEET 1 AB 3 PRO A 262 PRO A 264 0 SHEET 2 AB 3 GLY A 249 CYS A 256 -1 O ALA A 254 N PHE A 263 SHEET 3 AB 3 VAL A 287 ILE A 291 -1 O LYS A 288 N THR A 255 SHEET 1 AC 2 VAL A 324 GLU A 325 0 SHEET 2 AC 2 VAL B 1 MET B 2 -1 O VAL B 1 N GLU A 325 LINK NZ LYS B 0 CH XYQ B1000 1555 1555 1.37 LINK SG CYS A 256 ZN ZN A1409 1555 1555 2.43 LINK SG CYS A 259 ZN ZN A1409 1555 1555 2.14 LINK SG CYS A 280 ZN ZN A1409 1555 1555 2.23 LINK SG CYS A 283 ZN ZN A1409 1555 1555 2.26 CISPEP 1 GLU A 325 PRO A 326 0 2.59 SITE 1 AC1 26 GLY A 145 ALA A 146 GLY A 147 THR A 150 SITE 2 AC1 26 ASP A 156 PHE A 157 ARG A 158 TYR A 165 SITE 3 AC1 26 PHE A 180 GLN A 228 HIS A 248 VAL A 292 SITE 4 AC1 26 GLY A 319 THR A 320 SER A 321 VAL A 324 SITE 5 AC1 26 ASN A 344 ARG A 345 ASP A 346 GLY A 364 SITE 6 AC1 26 ASP A 365 VAL A 366 PEG A1408 HOH A2007 SITE 7 AC1 26 HOH A2019 LYS B 0 SITE 1 AC2 5 GLU A 181 VAL A 258 CYS A 259 GLN A 260 SITE 2 AC2 5 MET B 2 SITE 1 AC3 5 TYR A 200 PRO A 201 PHE A 251 GLY A 265 SITE 2 AC3 5 ARG A 269 SITE 1 AC4 1 HIS A 187 SITE 1 AC5 7 ASN A 229 ILE A 230 GLY A 232 GLU A 246 SITE 2 AC5 7 GLY A 249 THR A 250 PHE A 251 SITE 1 AC6 4 LYS A 190 VAL A 277 ARG A 279 ARG A 384 SITE 1 AC7 9 ALA A 146 SER A 149 ILE A 154 PHE A 157 SITE 2 AC7 9 ASN A 229 ILE A 230 ASP A 231 HOH A2019 SITE 3 AC7 9 HOH A2053 SITE 1 AC8 3 LYS A 205 THR A 391 HOH A2054 SITE 1 AC9 4 SER A 152 ASN A 203 TYR A 204 LYS A 205 SITE 1 BC1 5 GLN A 138 GLY A 220 LEU A 221 LEU A 222 SITE 2 BC1 5 LYS A 243 SITE 1 BC2 4 ARG A 276 GLY A 364 ASP A 365 HIS A 368 SITE 1 BC3 3 ARG A 224 SER A 242 ARG A 301 SITE 1 BC4 4 CYS A 283 ARG A 384 GLN A 388 HOH A2056 SITE 1 BC5 6 ARG A 158 SER A 159 PRO A 160 ARG A 345 SITE 2 BC5 6 ASP A 346 XYQ B1000 SITE 1 BC6 4 CYS A 256 CYS A 259 CYS A 280 CYS A 283 CRYST1 78.023 131.329 76.508 90.00 90.00 90.00 C 2 2 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 0.012817 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007614 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013071 0.00000