HEADER HYDROLASE 20-JUN-24 9CBT TITLE CRYSTAL STRUCTURE OF HUMAN SIRTUIN 3 FRAGMENT (RESIDUES 118-399) BOUND TITLE 2 TO INTERMEDIATES FROM REACTION WITH NAD AND INHIBITOR NH6-10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 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: SIRT3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PSUMO KEYWDS DEACETYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.K.FENWICK,H.J.YOUNG,H.LIN REVDAT 2 19-FEB-25 9CBT 1 JRNL REVDAT 1 07-AUG-24 9CBT 0 JRNL AUTH S.JANA,J.SHANG,J.Y.HONG,M.K.FENWICK,R.PURI,X.LU,A.M.MELNICK, JRNL AUTH 2 M.LI,H.LIN JRNL TITL A MITOCHONDRIA-TARGETING SIRT3 INHIBITOR WITH ACTIVITY JRNL TITL 2 AGAINST DIFFUSE LARGE B CELL LYMPHOMA. JRNL REF J.MED.CHEM. V. 67 15428 2024 JRNL REFN ISSN 0022-2623 JRNL PMID 39191393 JRNL DOI 10.1021/ACS.JMEDCHEM.4C01053 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 40071 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 2046 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.4300 - 4.8100 0.94 2550 122 0.1641 0.1838 REMARK 3 2 4.8100 - 3.8200 0.96 2551 133 0.1505 0.1898 REMARK 3 3 3.8200 - 3.3300 0.96 2476 164 0.1750 0.2057 REMARK 3 4 3.3300 - 3.0300 0.97 2534 139 0.1963 0.2145 REMARK 3 5 3.0300 - 2.8100 0.97 2530 131 0.1979 0.2638 REMARK 3 6 2.8100 - 2.6500 0.97 2534 133 0.2036 0.2385 REMARK 3 7 2.6500 - 2.5100 0.96 2529 121 0.2161 0.3003 REMARK 3 8 2.5100 - 2.4000 0.97 2470 180 0.2242 0.3068 REMARK 3 9 2.4000 - 2.3100 0.98 2558 118 0.2432 0.3057 REMARK 3 10 2.3100 - 2.2300 0.98 2588 121 0.2524 0.3395 REMARK 3 11 2.2300 - 2.1600 0.98 2541 123 0.2588 0.2827 REMARK 3 12 2.1600 - 2.1000 0.98 2539 124 0.2840 0.2911 REMARK 3 13 2.1000 - 2.0500 0.98 2520 177 0.3048 0.4052 REMARK 3 14 2.0500 - 2.0000 0.99 2561 135 0.3432 0.3780 REMARK 3 15 2.0000 - 1.9500 0.99 2544 125 0.3853 0.4377 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.57 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 122 THROUGH 189 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.5528 18.9178 11.8591 REMARK 3 T TENSOR REMARK 3 T11: 0.4777 T22: 0.3574 REMARK 3 T33: 0.5416 T12: 0.0507 REMARK 3 T13: 0.2507 T23: 0.0852 REMARK 3 L TENSOR REMARK 3 L11: 0.6927 L22: 1.6822 REMARK 3 L33: 3.6073 L12: -0.1436 REMARK 3 L13: -0.1465 L23: -1.4370 REMARK 3 S TENSOR REMARK 3 S11: 0.0677 S12: -0.0100 S13: 0.2133 REMARK 3 S21: -0.2016 S22: -0.1578 S23: -0.4061 REMARK 3 S31: 0.0001 S32: 0.0972 S33: 0.0833 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 190 THROUGH 207 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.0768 28.7361 23.9321 REMARK 3 T TENSOR REMARK 3 T11: 0.7067 T22: 0.3647 REMARK 3 T33: 0.6866 T12: -0.0368 REMARK 3 T13: 0.1554 T23: -0.0040 REMARK 3 L TENSOR REMARK 3 L11: 9.1378 L22: 5.2562 REMARK 3 L33: 4.2384 L12: -4.8482 REMARK 3 L13: 2.7695 L23: -4.4681 REMARK 3 S TENSOR REMARK 3 S11: -0.1913 S12: -0.5050 S13: 1.4554 REMARK 3 S21: 0.7858 S22: -0.4708 S23: -0.7148 REMARK 3 S31: -1.4803 S32: 0.0606 S33: 0.8265 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 208 THROUGH 255 OR RESID 257 REMARK 3 THROUGH 258 OR RESID 260 THROUGH 279 OR RESID 281 REMARK 3 THROUGH 282 OR RESID 284 THROUGH 391) REMARK 3 ORIGIN FOR THE GROUP (A): 15.9723 18.5227 12.4375 REMARK 3 T TENSOR REMARK 3 T11: 0.4222 T22: 0.3743 REMARK 3 T33: 0.4774 T12: 0.0283 REMARK 3 T13: 0.1687 T23: 0.0844 REMARK 3 L TENSOR REMARK 3 L11: 0.5256 L22: 0.5326 REMARK 3 L33: 3.2501 L12: 0.2316 REMARK 3 L13: 0.3594 L23: -0.6625 REMARK 3 S TENSOR REMARK 3 S11: 0.0582 S12: 0.1423 S13: 0.2423 REMARK 3 S21: -0.0182 S22: 0.0909 S23: 0.0579 REMARK 3 S31: -0.2463 S32: -0.1514 S33: -0.1368 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 122 THROUGH 189 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.3616 -5.7252 45.5816 REMARK 3 T TENSOR REMARK 3 T11: 0.1843 T22: 0.2442 REMARK 3 T33: 0.2944 T12: -0.0240 REMARK 3 T13: -0.0685 T23: -0.0309 REMARK 3 L TENSOR REMARK 3 L11: 2.7321 L22: 3.4240 REMARK 3 L33: 3.5381 L12: -0.5541 REMARK 3 L13: -2.0342 L23: -0.0667 REMARK 3 S TENSOR REMARK 3 S11: 0.2317 S12: -0.1085 S13: 0.1897 REMARK 3 S21: -0.2424 S22: -0.0737 S23: -0.4807 REMARK 3 S31: -0.1334 S32: 0.3404 S33: -0.1267 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 190 THROUGH 207 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.8838 -16.4193 34.4482 REMARK 3 T TENSOR REMARK 3 T11: 0.5817 T22: 0.3457 REMARK 3 T33: 0.5229 T12: 0.0112 REMARK 3 T13: -0.0458 T23: -0.0561 REMARK 3 L TENSOR REMARK 3 L11: 7.5358 L22: 3.5818 REMARK 3 L33: 6.4785 L12: 5.0887 REMARK 3 L13: -6.9767 L23: -4.7873 REMARK 3 S TENSOR REMARK 3 S11: -1.0865 S12: 0.8270 S13: -0.5151 REMARK 3 S21: -1.0963 S22: 0.5111 S23: -0.4210 REMARK 3 S31: 1.6567 S32: -0.7096 S33: 0.5534 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 208 THROUGH 255 OR RESID 257 REMARK 3 THROUGH 258 OR RESID 260 THROUGH 279 OR RESID 281 REMARK 3 THROUGH 282 OR RESID 284 THROUGH 327) REMARK 3 ORIGIN FOR THE GROUP (A): 14.4276 -3.8908 38.2184 REMARK 3 T TENSOR REMARK 3 T11: 0.2717 T22: 0.2525 REMARK 3 T33: 0.2907 T12: 0.0006 REMARK 3 T13: -0.0174 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.7660 L22: 1.4992 REMARK 3 L33: 3.5829 L12: 0.2775 REMARK 3 L13: -0.4281 L23: -0.6711 REMARK 3 S TENSOR REMARK 3 S11: 0.0410 S12: 0.1459 S13: 0.0484 REMARK 3 S21: -0.3072 S22: 0.0768 S23: -0.0473 REMARK 3 S31: 0.1542 S32: -0.0675 S33: -0.0988 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 328 THROUGH 395 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.8577 -4.8106 57.0567 REMARK 3 T TENSOR REMARK 3 T11: 0.2482 T22: 0.2254 REMARK 3 T33: 0.2031 T12: 0.0197 REMARK 3 T13: -0.0339 T23: 0.0139 REMARK 3 L TENSOR REMARK 3 L11: 2.5691 L22: 3.9833 REMARK 3 L33: 2.8989 L12: -0.7162 REMARK 3 L13: -0.1246 L23: -0.3802 REMARK 3 S TENSOR REMARK 3 S11: 0.0018 S12: -0.0770 S13: -0.1153 REMARK 3 S21: 0.1401 S22: 0.0934 S23: -0.2386 REMARK 3 S31: 0.0899 S32: 0.0670 S33: -0.0954 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9CBT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1000283142. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-21 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40149 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 39.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.88600 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: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS, PH 7.9, 100 MM MGCL2, 20 REMARK 280 % W/V PEG8000, AND 17.5 % W/V PEG400, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 31.59650 REMARK 290 SMTRY3 2 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 SER A 118 REMARK 465 ASP A 119 REMARK 465 LYS A 120 REMARK 465 GLY A 121 REMARK 465 GLY A 392 REMARK 465 LYS A 393 REMARK 465 LEU A 394 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 SER B 118 REMARK 465 ASP B 119 REMARK 465 LYS B 120 REMARK 465 GLY B 121 REMARK 465 GLY B 396 REMARK 465 PRO B 397 REMARK 465 ASP B 398 REMARK 465 LYS B 399 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 122 CG CD CE NZ REMARK 470 GLN A 170 CG CD OE1 NE2 REMARK 470 GLU A 177 CG CD OE1 OE2 REMARK 470 ASN A 203 CG OD1 ND2 REMARK 470 LYS A 205 CG CD CE NZ REMARK 470 GLN A 388 CG CD OE1 NE2 REMARK 470 THR A 391 OG1 CG2 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 GLN A 170 30.89 -85.10 REMARK 500 ASN A 207 -168.60 -115.22 REMARK 500 VAL A 258 -62.89 -103.83 REMARK 500 ASP A 290 47.60 -78.53 REMARK 500 ASN B 167 36.36 -140.01 REMARK 500 ASN B 207 -168.99 -108.60 REMARK 500 VAL B 258 -65.60 -104.16 REMARK 500 VAL B 282 -61.18 -96.45 REMARK 500 ASP B 290 45.34 -73.07 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 256 SG REMARK 620 2 CYS A 259 SG 108.2 REMARK 620 3 CYS A 280 SG 110.0 108.4 REMARK 620 4 CYS A 283 SG 101.3 118.3 110.3 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 256 SG REMARK 620 2 CYS B 259 SG 103.0 REMARK 620 3 CYS B 280 SG 104.0 104.9 REMARK 620 4 CYS B 283 SG 95.1 128.8 116.6 REMARK 620 N 1 2 3 DBREF 9CBT A 118 399 UNP Q9NTG7 SIR3_HUMAN 118 399 DBREF 9CBT B 118 399 UNP Q9NTG7 SIR3_HUMAN 118 399 SEQRES 1 A 282 SER ASP LYS GLY LYS LEU SER LEU GLN ASP VAL ALA GLU SEQRES 2 A 282 LEU ILE ARG ALA ARG ALA CYS GLN ARG VAL VAL VAL MET SEQRES 3 A 282 VAL GLY ALA GLY ILE SER THR PRO SER GLY ILE PRO ASP SEQRES 4 A 282 PHE ARG SER PRO GLY SER GLY LEU TYR SER ASN LEU GLN SEQRES 5 A 282 GLN TYR ASP LEU PRO TYR PRO GLU ALA ILE PHE GLU LEU SEQRES 6 A 282 PRO PHE PHE PHE HIS ASN PRO LYS PRO PHE PHE THR LEU SEQRES 7 A 282 ALA LYS GLU LEU TYR PRO GLY ASN TYR LYS PRO ASN VAL SEQRES 8 A 282 THR HIS TYR PHE LEU ARG LEU LEU HIS ASP LYS GLY LEU SEQRES 9 A 282 LEU LEU ARG LEU TYR THR GLN ASN ILE ASP GLY LEU GLU SEQRES 10 A 282 ARG VAL SER GLY ILE PRO ALA SER LYS LEU VAL GLU ALA SEQRES 11 A 282 HIS GLY THR PHE ALA SER ALA THR CYS THR VAL CYS GLN SEQRES 12 A 282 ARG PRO PHE PRO GLY GLU ASP ILE ARG ALA ASP VAL MET SEQRES 13 A 282 ALA ASP ARG VAL PRO ARG CYS PRO VAL CYS THR GLY VAL SEQRES 14 A 282 VAL LYS PRO ASP ILE VAL PHE PHE GLY GLU PRO LEU PRO SEQRES 15 A 282 GLN ARG PHE LEU LEU HIS VAL VAL ASP PHE PRO MET ALA SEQRES 16 A 282 ASP LEU LEU LEU ILE LEU GLY THR SER LEU GLU VAL GLU SEQRES 17 A 282 PRO PHE ALA SER LEU THR GLU ALA VAL ARG SER SER VAL SEQRES 18 A 282 PRO ARG LEU LEU ILE ASN ARG ASP LEU VAL GLY PRO LEU SEQRES 19 A 282 ALA TRP HIS PRO ARG SER ARG ASP VAL ALA GLN LEU GLY SEQRES 20 A 282 ASP VAL VAL HIS GLY VAL GLU SER LEU VAL GLU LEU LEU SEQRES 21 A 282 GLY TRP THR GLU GLU MET ARG ASP LEU VAL GLN ARG GLU SEQRES 22 A 282 THR GLY LYS LEU ASP GLY PRO ASP LYS SEQRES 1 B 282 SER ASP LYS GLY LYS LEU SER LEU GLN ASP VAL ALA GLU SEQRES 2 B 282 LEU ILE ARG ALA ARG ALA CYS GLN ARG VAL VAL VAL MET SEQRES 3 B 282 VAL GLY ALA GLY ILE SER THR PRO SER GLY ILE PRO ASP SEQRES 4 B 282 PHE ARG SER PRO GLY SER GLY LEU TYR SER ASN LEU GLN SEQRES 5 B 282 GLN TYR ASP LEU PRO TYR PRO GLU ALA ILE PHE GLU LEU SEQRES 6 B 282 PRO PHE PHE PHE HIS ASN PRO LYS PRO PHE PHE THR LEU SEQRES 7 B 282 ALA LYS GLU LEU TYR PRO GLY ASN TYR LYS PRO ASN VAL SEQRES 8 B 282 THR HIS TYR PHE LEU ARG LEU LEU HIS ASP LYS GLY LEU SEQRES 9 B 282 LEU LEU ARG LEU TYR THR GLN ASN ILE ASP GLY LEU GLU SEQRES 10 B 282 ARG VAL SER GLY ILE PRO ALA SER LYS LEU VAL GLU ALA SEQRES 11 B 282 HIS GLY THR PHE ALA SER ALA THR CYS THR VAL CYS GLN SEQRES 12 B 282 ARG PRO PHE PRO GLY GLU ASP ILE ARG ALA ASP VAL MET SEQRES 13 B 282 ALA ASP ARG VAL PRO ARG CYS PRO VAL CYS THR GLY VAL SEQRES 14 B 282 VAL LYS PRO ASP ILE VAL PHE PHE GLY GLU PRO LEU PRO SEQRES 15 B 282 GLN ARG PHE LEU LEU HIS VAL VAL ASP PHE PRO MET ALA SEQRES 16 B 282 ASP LEU LEU LEU ILE LEU GLY THR SER LEU GLU VAL GLU SEQRES 17 B 282 PRO PHE ALA SER LEU THR GLU ALA VAL ARG SER SER VAL SEQRES 18 B 282 PRO ARG LEU LEU ILE ASN ARG ASP LEU VAL GLY PRO LEU SEQRES 19 B 282 ALA TRP HIS PRO ARG SER ARG ASP VAL ALA GLN LEU GLY SEQRES 20 B 282 ASP VAL VAL HIS GLY VAL GLU SER LEU VAL GLU LEU LEU SEQRES 21 B 282 GLY TRP THR GLU GLU MET ARG ASP LEU VAL GLN ARG GLU SEQRES 22 B 282 THR GLY LYS LEU ASP GLY PRO ASP LYS HET ZN A 401 1 HET 5IA A 402 79 HET ZN B 401 1 HET PG4 B 402 13 HET 5I7 B 403 79 HETNAM ZN ZINC ION HETNAM 5IA 2-{[(2S)-6-[(Z)-(1-{[(2R,3R,4R,5R)-5-({[(R)-{[(R)- HETNAM 2 5IA {[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4- HETNAM 3 5IA DIHYDROXYOXOLAN-2-YL]METHOXY}(HYDROXY) HETNAM 4 5IA PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-4- HETNAM 5 5IA HYDROXY-2-SULFANYLOXOLAN-3-YL]OXY}TETRADECYLIDENE) HETNAM 6 5IA AMINO]-2-{[(BENZYLOXY)CARBONYL]AMINO}HEXANOYL]AMINO}- HETNAM 7 5IA N,N,N-TRIETHYLETHAN-1-AMINIUM (NON-PREFERRED NAME) HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM 5I7 (PHENYLMETHYL) ~{N}-[(2~{S})-6-[[(2~{R},3~{A}~{R}, HETNAM 2 5I7 5~{R},6~{R},6~{A}~{R})-5-[[[[(2~{R},3~{S},4~{R}, HETNAM 3 5I7 5~{R})-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN- HETNAM 4 5I7 2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL- HETNAM 5 5I7 PHOSPHORYL]OXYMETHYL]-6-OXIDANYL-2-TRIDECYL-3~{A},5,6, HETNAM 6 5I7 6~{A}-TETRAHYDROFURO[2,3-D][1,3]OXATHIOL-2-YL]AMINO]- HETNAM 7 5I7 1-OXIDANYLIDENE-1-[2-(TRIETHYL-$L^{4}-AZANYL) HETNAM 8 5I7 ETHYLAMINO]HEXAN-2-YL]CARBAMATE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 5IA C51 H86 N9 O16 P2 S 1+ FORMUL 6 PG4 C8 H18 O5 FORMUL 7 5I7 C51 H86 N9 O16 P2 S 1+ FORMUL 8 HOH *358(H2 O) HELIX 1 AA1 SER A 124 ALA A 134 1 11 HELIX 2 AA2 ALA A 146 GLY A 153 5 8 HELIX 3 AA3 GLY A 163 ASN A 167 5 5 HELIX 4 AA4 TYR A 175 PHE A 180 5 6 HELIX 5 AA5 GLU A 181 ASN A 188 1 8 HELIX 6 AA6 PRO A 189 TYR A 200 1 12 HELIX 7 AA7 ASN A 207 LYS A 219 1 13 HELIX 8 AA8 GLY A 232 SER A 237 1 6 HELIX 9 AA9 PRO A 240 SER A 242 5 3 HELIX 10 AB1 ILE A 268 ALA A 274 1 7 HELIX 11 AB2 PRO A 299 LEU A 303 5 5 HELIX 12 AB3 LEU A 304 ALA A 312 1 9 HELIX 13 AB4 PHE A 327 ALA A 333 5 7 HELIX 14 AB5 GLY A 349 HIS A 354 1 6 HELIX 15 AB6 ASP A 365 GLY A 378 1 14 HELIX 16 AB7 TRP A 379 THR A 391 1 13 HELIX 17 AB8 SER B 124 ALA B 134 1 11 HELIX 18 AB9 ALA B 146 GLY B 153 5 8 HELIX 19 AC1 GLY B 163 ASN B 167 5 5 HELIX 20 AC2 TYR B 175 PHE B 180 5 6 HELIX 21 AC3 GLU B 181 ASN B 188 1 8 HELIX 22 AC4 PRO B 189 LEU B 199 1 11 HELIX 23 AC5 ASN B 207 LYS B 219 1 13 HELIX 24 AC6 GLY B 232 SER B 237 1 6 HELIX 25 AC7 PRO B 240 SER B 242 5 3 HELIX 26 AC8 ILE B 268 ALA B 274 1 7 HELIX 27 AC9 PRO B 299 LEU B 303 5 5 HELIX 28 AD1 LEU B 304 ALA B 312 1 9 HELIX 29 AD2 PHE B 327 ALA B 333 5 7 HELIX 30 AD3 VAL B 348 HIS B 354 1 7 HELIX 31 AD4 ASP B 365 GLY B 378 1 14 HELIX 32 AD5 TRP B 379 ASP B 395 1 17 SHEET 1 AA1 6 LEU A 244 GLU A 246 0 SHEET 2 AA1 6 LEU A 222 THR A 227 1 N THR A 227 O VAL A 245 SHEET 3 AA1 6 VAL A 140 VAL A 144 1 N VAL A 142 O TYR A 226 SHEET 4 AA1 6 LEU A 314 LEU A 318 1 O LEU A 316 N MET A 143 SHEET 5 AA1 6 ARG A 340 ASN A 344 1 O LEU A 341 N LEU A 315 SHEET 6 AA1 6 ASP A 359 LEU A 363 1 O GLN A 362 N LEU A 342 SHEET 1 AA2 3 PRO A 262 PRO A 264 0 SHEET 2 AA2 3 GLY A 249 CYS A 256 -1 N ALA A 254 O PHE A 263 SHEET 3 AA2 3 VAL A 287 ILE A 291 -1 O LYS A 288 N THR A 255 SHEET 1 AA3 6 LEU B 244 GLU B 246 0 SHEET 2 AA3 6 LEU B 222 THR B 227 1 N LEU B 225 O VAL B 245 SHEET 3 AA3 6 VAL B 140 VAL B 144 1 N VAL B 142 O TYR B 226 SHEET 4 AA3 6 LEU B 314 LEU B 318 1 O LEU B 316 N MET B 143 SHEET 5 AA3 6 ARG B 340 ASN B 344 1 O LEU B 341 N LEU B 315 SHEET 6 AA3 6 ASP B 359 LEU B 363 1 O VAL B 360 N LEU B 342 SHEET 1 AA4 3 PRO B 262 PRO B 264 0 SHEET 2 AA4 3 GLY B 249 CYS B 256 -1 N ALA B 254 O PHE B 263 SHEET 3 AA4 3 VAL B 287 ILE B 291 -1 O ASP B 290 N SER B 253 LINK SG CYS A 256 ZN ZN A 401 1555 1555 2.32 LINK SG CYS A 259 ZN ZN A 401 1555 1555 2.29 LINK SG CYS A 280 ZN ZN A 401 1555 1555 2.33 LINK SG CYS A 283 ZN ZN A 401 1555 1555 2.30 LINK SG CYS B 256 ZN ZN B 401 1555 1555 2.30 LINK SG CYS B 259 ZN ZN B 401 1555 1555 2.30 LINK SG CYS B 280 ZN ZN B 401 1555 1555 2.31 LINK SG CYS B 283 ZN ZN B 401 1555 1555 2.29 CISPEP 1 GLU A 325 PRO A 326 0 1.75 CISPEP 2 GLU B 325 PRO B 326 0 -1.04 CRYST1 39.433 63.193 114.608 90.00 90.79 90.00 P 1 21 1 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 0.025359 0.000000 0.000348 0.00000 SCALE2 0.000000 0.015825 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008726 0.00000