HEADER HYDROLASE/INHIBITOR 09-AUG-17 5Y5N TITLE CRYSTAL STRUCTURE OF HUMAN SIRTUIN 2 IN COMPLEX WITH A SELECTIVE TITLE 2 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: REGULATORY PROTEIN SIR2 HOMOLOG 2,SIR2-LIKE PROTEIN 2; COMPND 5 EC: 3.5.1.-; COMPND 6 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: SIRT2, SIR2L, SIR2L2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PSEUDOPEPTIDES, ANTICANCER ACTIVITY, NEURITE OUTGROWTH, HYDROLASE- KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.MELLINI,Y.ITOH,H.TSUMOTO,Y.LI,M.SUZUKI,N.TOKUDA,T.KAKIZAWA,Y.MIURA, AUTHOR 2 J.TAKEUCHI,M.LAHTELA-KAKKONEN,T.SUZUKI REVDAT 3 22-NOV-23 5Y5N 1 REMARK REVDAT 2 18-DEC-19 5Y5N 1 JRNL REVDAT 1 06-SEP-17 5Y5N 0 JRNL AUTH P.MELLINI,Y.ITOH,H.TSUMOTO,Y.LI,M.SUZUKI,N.TOKUDA, JRNL AUTH 2 T.KAKIZAWA,Y.MIURA,J.TAKEUCHI,M.LAHTELA-KAKKONEN,T.SUZUKI JRNL TITL POTENT MECHANISM-BASED SIRTUIN-2-SELECTIVE INHIBITION BY JRNL TITL 2 ANIN SITU-GENERATED OCCUPANT OF THE SUBSTRATE-BINDING SITE, JRNL TITL 3 "SELECTIVITY POCKET" AND NAD+-BINDING SITE. JRNL REF CHEM SCI V. 8 6400 2017 JRNL REFN ISSN 2041-6520 JRNL PMID 28989670 JRNL DOI 10.1039/C7SC02738A REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2005 PARALLEL (OPEN MP) REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 17089 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.256 REMARK 3 R VALUE (WORKING SET) : 0.256 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2290 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 102 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AUTHORS STATE THAT R-WORK(0.256) IS REMARK 3 HIGHER THAN R-FREE(0.252) DUE TO A RARE CASE REMARK 4 REMARK 4 5Y5N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1300004615. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17089 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 42.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 1J8F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS BUFFER PH 5.5 15%(W/V) REMARK 280 PEG5000 MME, VAPOR DIFFUSION, TEMPERATURE 289K 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 25.42500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.26600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.99000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.26600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.42500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.99000 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: MONOMERIC 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 GLY A 32 REMARK 465 SER A 33 REMARK 465 SER A 100 REMARK 465 THR A 101 REMARK 465 GLY A 102 REMARK 465 LEU A 103 REMARK 465 TYR A 104 REMARK 465 ASP A 105 REMARK 465 ASN A 106 REMARK 465 LEU A 107 REMARK 465 GLU A 108 REMARK 465 LYS A 109 REMARK 465 TYR A 110 REMARK 465 LYS A 288A REMARK 465 ALA A 288B REMARK 465 GLY A 288C REMARK 465 GLN A 288D REMARK 465 SER A 288E REMARK 465 ASP A 288F REMARK 465 PRO A 288G REMARK 465 PHE A 288H REMARK 465 LEU A 288I REMARK 465 GLY A 288J REMARK 465 MET A 288K REMARK 465 ILE A 288L REMARK 465 MET A 288M REMARK 465 GLY A 288N REMARK 465 LEU A 288O REMARK 465 GLY A 288P REMARK 465 GLY A 288Q REMARK 465 GLY A 288R REMARK 465 MET A 288S REMARK 465 ASP A 288T REMARK 465 LEU A 288U REMARK 465 GLY A 288V REMARK 465 GLU A 288W REMARK 465 THR A 288X REMARK 465 PRO A 288Y REMARK 465 PHE A 288Z REMARK 465 ASP A 289A REMARK 465 ASP A 289B REMARK 465 ILE A 289C REMARK 465 ALA A 289D REMARK 465 THR A 289E REMARK 465 PHE A 289F REMARK 465 ASP A 289G REMARK 465 SER A 289H REMARK 465 LYS A 289I 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 LEU A 239 CG CD1 CD2 REMARK 470 LYS A 313 CG CD CE NZ REMARK 470 GLN A 326 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 1133 O HOH A 1147 1.52 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 1115 O HOH A 1189 2674 1.33 REMARK 500 O HOH A 1102 O HOH A 1127 4565 1.47 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 112 CA - CB - CG ANGL. DEV. = 20.0 DEGREES REMARK 500 PRO A 268 N - CA - C ANGL. DEV. = 15.8 DEGREES REMARK 500 ARG A 347 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 347 NE - CZ - NH2 ANGL. DEV. = -3.3 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 PRO A 113 -93.19 -39.33 REMARK 500 ASP A 170 -9.41 -58.56 REMARK 500 THR A 171 -5.49 73.42 REMARK 500 CYS A 200 -62.17 -143.74 REMARK 500 ARG A 201 27.14 47.71 REMARK 500 GLN A 225 11.53 58.13 REMARK 500 ASP A 231 40.87 -71.65 REMARK 500 ALA A 314 133.63 -39.55 REMARK 500 TYR A 315 -15.25 -143.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 347 0.11 SIDE CHAIN 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 195 SG REMARK 620 2 CYS A 200 SG 103.7 REMARK 620 3 CYS A 221 SG 110.6 116.7 REMARK 620 4 CYS A 224 SG 85.0 112.0 122.3 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 8NO A 1002 REMARK 999 REMARK 999 SEQUENCE REMARK 999 GS RESIDUES OF N TERMINAL ARE REST OF THROMBIN RECOGNITION REMARK 999 SEQUENCE. FROM LYS289 TO LYS312 ARE MISSING AND IN THIS REGION, THE REMARK 999 RESIDUES LGETPFDDIAT FROM SIR2 HOMOLOG (PDB ID : 3JR3) ARE INSERTED. DBREF 5Y5N A 34 356 UNP Q8IXJ6 SIR2_HUMAN 34 356 SEQADV 5Y5N GLY A 32 UNP Q8IXJ6 SEE SEQUENCE DETAILS SEQADV 5Y5N SER A 33 UNP Q8IXJ6 SEE SEQUENCE DETAILS SEQADV 5Y5N LEU A 288U UNP Q8IXJ6 SEE SEQUENCE DETAILS SEQADV 5Y5N GLY A 288V UNP Q8IXJ6 SEE SEQUENCE DETAILS SEQADV 5Y5N GLU A 288W UNP Q8IXJ6 SEE SEQUENCE DETAILS SEQADV 5Y5N THR A 288X UNP Q8IXJ6 SEE SEQUENCE DETAILS SEQADV 5Y5N PRO A 288Y UNP Q8IXJ6 SEE SEQUENCE DETAILS SEQADV 5Y5N PHE A 288Z UNP Q8IXJ6 SEE SEQUENCE DETAILS SEQADV 5Y5N ASP A 289A UNP Q8IXJ6 SEE SEQUENCE DETAILS SEQADV 5Y5N ASP A 289B UNP Q8IXJ6 SEE SEQUENCE DETAILS SEQADV 5Y5N ILE A 289C UNP Q8IXJ6 SEE SEQUENCE DETAILS SEQADV 5Y5N ALA A 289D UNP Q8IXJ6 SEE SEQUENCE DETAILS SEQADV 5Y5N THR A 289E UNP Q8IXJ6 SEE SEQUENCE DETAILS SEQRES 1 A 336 GLY SER GLY GLU ALA ASP MET ASP PHE LEU ARG ASN LEU SEQRES 2 A 336 PHE SER GLN THR LEU SER LEU GLY SER GLN LYS GLU ARG SEQRES 3 A 336 LEU LEU ASP GLU LEU THR LEU GLU GLY VAL ALA ARG TYR SEQRES 4 A 336 MET GLN SER GLU ARG CYS ARG ARG VAL ILE CYS LEU VAL SEQRES 5 A 336 GLY ALA GLY ILE SER THR SER ALA GLY ILE PRO ASP PHE SEQRES 6 A 336 ARG SER PRO SER THR GLY LEU TYR ASP ASN LEU GLU LYS SEQRES 7 A 336 TYR HIS LEU PRO TYR PRO GLU ALA ILE PHE GLU ILE SER SEQRES 8 A 336 TYR PHE LYS LYS HIS PRO GLU PRO PHE PHE ALA LEU ALA SEQRES 9 A 336 LYS GLU LEU TYR PRO GLY GLN PHE LYS PRO THR ILE CYS SEQRES 10 A 336 HIS TYR PHE MET ARG LEU LEU LYS ASP LYS GLY LEU LEU SEQRES 11 A 336 LEU ARG CYS TYR THR GLN ASN ILE ASP THR LEU GLU ARG SEQRES 12 A 336 ILE ALA GLY LEU GLU GLN GLU ASP LEU VAL GLU ALA HIS SEQRES 13 A 336 GLY THR PHE TYR THR SER HIS CYS VAL SER ALA SER CYS SEQRES 14 A 336 ARG HIS GLU TYR PRO LEU SER TRP MET LYS GLU LYS ILE SEQRES 15 A 336 PHE SER GLU VAL THR PRO LYS CYS GLU ASP CYS GLN SER SEQRES 16 A 336 LEU VAL LYS PRO ASP ILE VAL PHE PHE GLY GLU SER LEU SEQRES 17 A 336 PRO ALA ARG PHE PHE SER CYS MET GLN SER ASP PHE LEU SEQRES 18 A 336 LYS VAL ASP LEU LEU LEU VAL MET GLY THR SER LEU GLN SEQRES 19 A 336 VAL GLN PRO PHE ALA SER LEU ILE SER LYS ALA PRO LEU SEQRES 20 A 336 SER THR PRO ARG LEU LEU ILE ASN LYS GLU LYS ALA GLY SEQRES 21 A 336 GLN SER ASP PRO PHE LEU GLY MET ILE MET GLY LEU GLY SEQRES 22 A 336 GLY GLY MET ASP LEU GLY GLU THR PRO PHE ASP ASP ILE SEQRES 23 A 336 ALA THR PHE ASP SER LYS LYS ALA TYR ARG ASP VAL ALA SEQRES 24 A 336 TRP LEU GLY GLU CYS ASP GLN GLY CYS LEU ALA LEU ALA SEQRES 25 A 336 GLU LEU LEU GLY TRP LYS LYS GLU LEU GLU ASP LEU VAL SEQRES 26 A 336 ARG ARG GLU HIS ALA SER ILE ASP ALA GLN SER HET ZN A1001 1 HET 8NO A1002 25 HETNAM ZN ZINC ION HETNAM 8NO 2-[[3-(2-PHENYLETHOXY)PHENYL]AMINO]BENZAMIDE FORMUL 2 ZN ZN 2+ FORMUL 3 8NO C21 H20 N2 O2 FORMUL 4 HOH *102(H2 O) HELIX 1 AA1 GLY A 34 GLY A 52 1 19 HELIX 2 AA2 THR A 63 SER A 73 1 11 HELIX 3 AA3 ALA A 85 GLY A 92 5 8 HELIX 4 AA4 TYR A 114 PHE A 119 5 6 HELIX 5 AA5 GLU A 120 HIS A 127 1 8 HELIX 6 AA6 PRO A 128 TYR A 139 1 12 HELIX 7 AA7 THR A 146 LYS A 158 1 13 HELIX 8 AA8 THR A 171 ALA A 176 1 6 HELIX 9 AA9 GLU A 179 GLU A 181 5 3 HELIX 10 AB1 LEU A 206 GLU A 216 1 11 HELIX 11 AB2 ALA A 241 PHE A 251 1 11 HELIX 12 AB3 PRO A 268 SER A 274 1 7 HELIX 13 AB4 GLU A 323 LEU A 335 1 13 HELIX 14 AB5 TRP A 337 ALA A 354 1 18 SHEET 1 AA1 6 LEU A 183 GLU A 185 0 SHEET 2 AA1 6 LEU A 161 THR A 166 1 N THR A 166 O VAL A 184 SHEET 3 AA1 6 VAL A 79 VAL A 83 1 N CYS A 81 O TYR A 165 SHEET 4 AA1 6 LEU A 256 MET A 260 1 O LEU A 258 N LEU A 82 SHEET 5 AA1 6 ARG A 282 ASN A 286 1 O LEU A 283 N LEU A 257 SHEET 6 AA1 6 ASP A 317 LEU A 321 1 O TRP A 320 N LEU A 284 SHEET 1 AA2 3 GLU A 203 PRO A 205 0 SHEET 2 AA2 3 GLY A 188 CYS A 195 -1 N SER A 193 O TYR A 204 SHEET 3 AA2 3 VAL A 228 ILE A 232 -1 O LYS A 229 N HIS A 194 LINK SG CYS A 195 ZN ZN A1001 1555 1555 2.18 LINK SG CYS A 200 ZN ZN A1001 1555 1555 2.00 LINK SG CYS A 221 ZN ZN A1001 1555 1555 2.08 LINK SG CYS A 224 ZN ZN A1001 1555 1555 2.27 CISPEP 1 GLN A 267 PRO A 268 0 -0.08 SITE 1 AC1 4 CYS A 195 CYS A 200 CYS A 221 CYS A 224 SITE 1 AC2 10 PHE A 96 PHE A 119 PHE A 131 PRO A 140 SITE 2 AC2 10 PHE A 143 ILE A 169 PHE A 190 VAL A 233 SITE 3 AC2 10 HOH A1112 HOH A1119 CRYST1 50.850 57.980 124.532 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 0.019666 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017247 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008030 0.00000