HEADER HYDROLASE 24-JUN-13 4BUZ TITLE SIR2 COMPLEX STRUCTURE MIXTURE OF EX-527 INHIBITOR AND REACTION TITLE 2 PRODUCTS OR OF REACTION SUBSTRATES P53 PEPTIDE AND NAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACETYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: REGULATORY PROTEIN SIR2 HOMOLOG, SIR2TM, NAD-DEPENDENT COMPND 5 PROTEIN DEACETYLASE SIR2; COMPND 6 EC: 3.5.1.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 10 CHAIN: P; COMPND 11 FRAGMENT: RESIDUES 379-386; COMPND 12 SYNONYM: ANTIGEN NY-CO-13, PHOSPHOPROTEIN P53, TUMOR SUPPRESSOR P53, COMPND 13 P53; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: ACETYLATED P53 LYS-382 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS HYDROLASE, NAD-DEPENDENT DEACETYLASE, SIRTUIN, INHIBITOR COMPLEX, EX- KEYWDS 2 527, RUNNING REACTION EXPDTA X-RAY DIFFRACTION AUTHOR M.WEYAND,M.LAKSHMINARASIMHAN,M.GERTZ,C.STEEGBORN REVDAT 3 20-DEC-23 4BUZ 1 REMARK LINK REVDAT 2 07-AUG-13 4BUZ 1 JRNL REVDAT 1 17-JUL-13 4BUZ 0 JRNL AUTH M.GERTZ,F.FISCHER,G.T.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.USA V. 110 E2772 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23840057 JRNL DOI 10.1073/PNAS.1303628110 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 23580 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1241 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) : 1746 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1928 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 105 REMARK 3 SOLVENT ATOMS : 200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.99000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : -0.83000 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): 0.124 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.118 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.883 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2183 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2112 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2978 ; 2.065 ; 2.047 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4885 ; 1.010 ; 3.008 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 269 ; 6.187 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 95 ;38.253 ;23.895 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 389 ;14.022 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;19.676 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 338 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2391 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 485 ; 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): 1010 ; 2.122 ; 1.819 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1009 ; 2.115 ; 1.814 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1268 ; 3.258 ; 2.694 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1173 ; 2.829 ; 2.261 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 36 REMARK 3 RESIDUE RANGE : A 75 A 115 REMARK 3 RESIDUE RANGE : A 166 A 246 REMARK 3 ORIGIN FOR THE GROUP (A): -3.2233 9.0989 -9.9847 REMARK 3 T TENSOR REMARK 3 T11: 0.0277 T22: 0.0214 REMARK 3 T33: 0.0304 T12: -0.0097 REMARK 3 T13: 0.0188 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 0.3967 L22: 0.9262 REMARK 3 L33: 1.4542 L12: -0.0641 REMARK 3 L13: -0.0938 L23: -0.1796 REMARK 3 S TENSOR REMARK 3 S11: -0.0708 S12: 0.0095 S13: -0.0642 REMARK 3 S21: -0.0765 S22: 0.0251 S23: -0.0017 REMARK 3 S31: 0.1222 S32: -0.0331 S33: 0.0457 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 44 A 73 REMARK 3 RESIDUE RANGE : A 116 A 161 REMARK 3 ORIGIN FOR THE GROUP (A): 5.1050 35.9194 -15.1737 REMARK 3 T TENSOR REMARK 3 T11: 0.0672 T22: 0.0343 REMARK 3 T33: 0.0422 T12: -0.0014 REMARK 3 T13: 0.0026 T23: 0.0217 REMARK 3 L TENSOR REMARK 3 L11: 0.6579 L22: 1.7050 REMARK 3 L33: 2.5823 L12: -0.3413 REMARK 3 L13: 0.6045 L23: -0.9340 REMARK 3 S TENSOR REMARK 3 S11: -0.0068 S12: 0.0934 S13: 0.0952 REMARK 3 S21: 0.1389 S22: -0.1019 S23: -0.2174 REMARK 3 S31: -0.2149 S32: -0.0616 S33: 0.1087 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 WITH TLS ADDED REMARK 4 REMARK 4 4BUZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1290057413. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-11 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 : 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) : 0.919980 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 : 24822 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 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 2H4F REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8.5, PH 8.5 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 23.37500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.51500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.96000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.51500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.37500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.96000 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: 1950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P 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 LYS P 386 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 45 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 HOH A 2146 O HOH A 2147 2.01 REMARK 500 O HOH A 2064 O HOH A 2068 2.15 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 OE2 GLU A 121 O HOH A 2191 4555 2.18 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 ASP A 51 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 222 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 MET A 240 CG - SD - CE ANGL. DEV. = -14.4 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 SER A 44 115.99 71.89 REMARK 500 ILE A 68 -59.65 -130.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 245 SER A 246 148.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2076 DISTANCE = 5.85 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE INHIBITOR OCZ (A1247), ACETYLATED LYSINE ALY (P 382) AND REMARK 600 SUBSTRATE ACETYL RIBOSE OAD (A 1249) BIND ALTERNATIVELY TO REMARK 600 THE SAME BINDING SITE GIVING RISE TO MICROHETEROGENEITY. 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 A1250 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 124 SG REMARK 620 2 CYS A 127 SG 114.5 REMARK 620 3 CYS A 148 SG 100.9 109.1 REMARK 620 4 CYS A 151 SG 95.6 120.5 113.8 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 OCZ A 1247 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 1248 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OAD A 1249 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1250 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1251 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BV2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH THE INHIBITOR EX-527, 2'- REMARK 900 O-ACETYL-ADP-RIBOSE AND DEACETYLATED P53-PEPTIDE 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 THE INHIBITOR EX- REMARK 900 527 AND ADP-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: 4BVG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH NATIVE REMARK 900 ALKYLIMIDATE FORMED FROM ACETYL-LYSINE ACS2- PEPTIDE CRYSTALLIZED REMARK 900 IN 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 DBREF 4BUZ A 1 246 UNP Q9WYW0 NPD_THEMA 1 246 DBREF 4BUZ P 379 386 UNP P04637 P53_HUMAN 379 386 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 P 8 ARG HIS LYS ALY LEU MET PHE LYS MODRES 4BUZ ALY P 382 LYS N(6)-ACETYLLYSINE HET ALY P 382 12 HET OCZ A1247 17 HET NAD A1248 44 HET OAD A1249 39 HET ZN A1250 1 HET EDO A1251 4 HETNAM ALY N(6)-ACETYLLYSINE HETNAM OCZ (1S)-6-CHLORO-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-1- HETNAM 2 OCZ CARBOXAMIDE HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ALY C8 H16 N2 O3 FORMUL 3 OCZ C13 H13 CL N2 O FORMUL 4 NAD C21 H27 N7 O14 P2 FORMUL 5 OAD C17 H25 N5 O15 P2 FORMUL 6 ZN ZN 2+ FORMUL 7 EDO C2 H6 O2 FORMUL 8 HOH *200(H2 O) HELIX 1 1 MET A 3 SER A 13 1 11 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 ALA A 74 5 6 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 ALA A 197 SER A 206 1 10 HELIX 11 11 PHE A 220 ALA A 224 5 5 HELIX 12 12 ASP A 231 GLY A 243 1 13 SHEET 1 AA 6 VAL A 112 GLU A 114 0 SHEET 2 AA 6 ALA A 94 THR A 97 1 O VAL A 95 N ILE A 113 SHEET 3 AA 6 THR A 16 THR A 20 1 O THR A 18 N ILE A 96 SHEET 4 AA 6 LEU A 183 LEU A 187 1 O LEU A 183 N VAL A 17 SHEET 5 AA 6 LYS A 209 VAL A 213 1 O LYS A 209 N MET A 184 SHEET 6 AA 6 LEU A 226 TYR A 228 1 O LEU A 226 N ILE A 212 SHEET 1 AB 3 LYS A 130 THR A 132 0 SHEET 2 AB 3 GLY A 117 CYS A 124 -1 O TYR A 122 N TYR A 131 SHEET 3 AB 3 ILE A 155 ILE A 159 -1 O ARG A 156 N TYR A 123 SHEET 1 AC 2 VAL A 193 TYR A 194 0 SHEET 2 AC 2 LEU P 383 MET P 384 -1 O LEU P 383 N TYR A 194 LINK C LYS P 381 N ALY P 382 1555 1555 1.32 LINK C ALY P 382 N LEU P 383 1555 1555 1.32 LINK SG CYS A 124 ZN ZN A1250 1555 1555 2.34 LINK SG CYS A 127 ZN ZN A1250 1555 1555 2.29 LINK SG CYS A 148 ZN ZN A1250 1555 1555 2.29 LINK SG CYS A 151 ZN ZN A1250 1555 1555 2.38 CISPEP 1 TYR A 194 PRO A 195 0 1.05 SITE 1 AC1 13 PRO A 31 PHE A 33 PHE A 48 MET A 71 SITE 2 AC1 13 GLN A 98 ASN A 99 ILE A 100 ASP A 101 SITE 3 AC1 13 ILE A 159 VAL A 160 HOH A2020 HOH A2021 SITE 4 AC1 13 ALY P 382 SITE 1 AC2 28 GLY A 21 ALA A 22 GLY A 23 THR A 26 SITE 2 AC2 28 PRO A 27 ILE A 30 PRO A 31 ASP A 32 SITE 3 AC2 28 PHE A 33 GLN A 98 ASN A 99 ILE A 100 SITE 4 AC2 28 ASP A 101 HIS A 116 GLY A 188 SER A 189 SITE 5 AC2 28 SER A 190 ASN A 214 LEU A 215 MET A 230 SITE 6 AC2 28 ASP A 231 VAL A 232 HOH A2020 HOH A2021 SITE 7 AC2 28 HOH A2161 HOH A2196 HOH A2197 ALY P 382 SITE 1 AC3 25 GLY A 21 ALA A 22 GLY A 23 THR A 26 SITE 2 AC3 25 PRO A 27 ASP A 32 PHE A 33 PHE A 48 SITE 3 AC3 25 HIS A 116 VAL A 160 PHE A 162 GLY A 188 SITE 4 AC3 25 SER A 189 SER A 190 VAL A 193 ASN A 214 SITE 5 AC3 25 LEU A 215 MET A 230 ASP A 231 VAL A 232 SITE 6 AC3 25 HOH A2020 HOH A2161 HOH A2196 HOH A2197 SITE 7 AC3 25 ALY P 382 SITE 1 AC4 4 CYS A 124 CYS A 127 CYS A 148 CYS A 151 SITE 1 AC5 4 TYR A 123 LYS A 130 HOH A2107 HOH A2114 CRYST1 46.750 59.920 109.030 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 0.021390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016689 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009172 0.00000