PDB Short entry for 4HD8 HEADER HYDROLASE/HYDROLASE INHIBITOR 02-OCT-12 4HD8 TITLE CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH FLUOR-DE-LYS PEPTIDE TITLE 2 AND PICEATANNOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 116-399; COMPND 5 SYNONYM: HSIRT3, REGULATORY PROTEIN SIR2 HOMOLOG 3, SIR2-LIKE PROTEIN COMPND 6 3; COMPND 7 EC: 3.5.1.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: FLUOR-DE-LYS PEPTIDE; COMPND 11 CHAIN: F; COMPND 12 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: SIR2L3, SIRT3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) 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 OTHER_DETAILS: COUMARIN-MODIFIED TETRA PEPTIDE KEYWDS NAD-DEPENDENT DEACETYLASE, SIRTUIN, MITOCHONDRIAL, INHIBITOR COMPLEX, KEYWDS 2 PICEATANNOL, RESVERATROL-LIKE COMPOUND, HYDROLASE-HYDROLASE KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.T.T.NGUYEN,M.GERTZ,C.STEEGBORN REVDAT 3 28-FEB-24 4HD8 1 REMARK LINK REVDAT 2 20-FEB-13 4HD8 1 JRNL REVDAT 1 05-DEC-12 4HD8 0 JRNL AUTH M.GERTZ,G.T.NGUYEN,F.FISCHER,B.SUENKEL,C.SCHLICKER, JRNL AUTH 2 B.FRANZEL,J.TOMASCHEWSKI,F.ALADINI,C.BECKER,D.WOLTERS, JRNL AUTH 3 C.STEEGBORN JRNL TITL A MOLECULAR MECHANISM FOR DIRECT SIRTUIN ACTIVATION BY JRNL TITL 2 RESVERATROL. JRNL REF PLOS ONE V. 7 49761 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 23185430 JRNL DOI 10.1371/JOURNAL.PONE.0049761 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 14069 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 704 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 979 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2102 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 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) : 31.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.31000 REMARK 3 B22 (A**2) : 0.31000 REMARK 3 B33 (A**2) : -1.00000 REMARK 3 B12 (A**2) : 0.31000 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): 0.291 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.231 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.149 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.066 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2203 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3004 ; 1.892 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 269 ; 6.333 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 95 ;38.312 ;22.737 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 356 ;16.568 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;17.168 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 338 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1689 ; 0.010 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 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 USED IF PRESENT IN REMARK 3 THE INPUT. U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 4HD8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075319. 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 : 7 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14069 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 38.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.48700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM NACL, 100 MM HEPES PH 7, 10% REMARK 280 (V/V) ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 57.30000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.08217 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 41.23333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 57.30000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 33.08217 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 41.23333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 57.30000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 33.08217 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 41.23333 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 57.30000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 33.08217 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 41.23333 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 57.30000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 33.08217 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 41.23333 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 57.30000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 33.08217 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 41.23333 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 66.16434 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 82.46667 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 66.16434 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 82.46667 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 66.16434 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 82.46667 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 66.16434 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 82.46667 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 66.16434 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 82.46667 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 66.16434 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 82.46667 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 APPLY THE FOLLOWING TO CHAINS: A, F 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 ARG A 158 REMARK 465 SER A 159 REMARK 465 PRO A 160 REMARK 465 GLY A 161 REMARK 465 SER A 162 REMARK 465 GLY A 163 REMARK 465 LEU A 164 REMARK 465 TYR A 165 REMARK 465 SER A 166 REMARK 465 ASN A 167 REMARK 465 LEU A 168 REMARK 465 GLN A 169 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 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 VAL A 258 -60.03 -104.95 REMARK 500 THR A 284 -6.03 69.41 REMARK 500 PRO A 289 152.67 -45.36 REMARK 500 ASP A 290 49.07 -83.80 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 110.2 REMARK 620 3 CYS A 280 SG 107.8 107.7 REMARK 620 4 CYS A 283 SG 94.4 120.2 115.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PIT A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN F OF FLUOR-DE-LYS PEPTIDE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HDA RELATED DB: PDB DBREF 4HD8 A 116 399 UNP Q9NTG7 SIR3_HUMAN 116 399 DBREF 4HD8 F 1 4 PDB 4HD8 4HD8 1 4 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 F 4 ARG HIS LYS FDL MODRES 4HD8 FDL F 4 LYS HET FDL F 4 25 HET ZN A 401 1 HET PIT A 402 18 HET IPA A 403 4 HETNAM FDL N~6~-ACETYL-N-(4-METHYL-2-OXO-2H-CHROMEN-7-YL)-L- HETNAM 2 FDL LYSINAMIDE HETNAM ZN ZINC ION HETNAM PIT PICEATANNOL HETNAM IPA ISOPROPYL ALCOHOL HETSYN PIT 4-[(E)-2-(3,5-DIHYDROXYPHENYL)ETHENYL]BENZENE-1,2-DIOL HETSYN IPA 2-PROPANOL FORMUL 2 FDL C18 H23 N3 O4 FORMUL 3 ZN ZN 2+ FORMUL 4 PIT C14 H12 O4 FORMUL 5 IPA C3 H8 O FORMUL 6 HOH *102(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 TYR A 200 1 12 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 GLY A 265 ALA A 274 1 10 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 PRO A 326 GLU A 332 1 7 HELIX 13 13 GLY A 349 HIS A 354 1 6 HELIX 14 14 ASP A 365 GLY A 378 1 14 HELIX 15 15 TRP A 379 GLY A 392 1 14 SHEET 1 A 6 LEU A 244 GLU A 246 0 SHEET 2 A 6 LEU A 222 THR A 227 1 N LEU A 225 O VAL A 245 SHEET 3 A 6 VAL A 140 VAL A 144 1 N VAL A 142 O TYR A 226 SHEET 4 A 6 LEU A 314 LEU A 318 1 O LEU A 316 N MET A 143 SHEET 5 A 6 ARG A 340 ASN A 344 1 O LEU A 341 N LEU A 315 SHEET 6 A 6 ASP A 359 LEU A 363 1 O GLN A 362 N LEU A 342 SHEET 1 B 3 PRO A 262 PRO A 264 0 SHEET 2 B 3 GLY A 249 CYS A 256 -1 N ALA A 254 O PHE A 263 SHEET 3 B 3 VAL A 287 ILE A 291 -1 O ASP A 290 N SER A 253 LINK SG CYS A 256 ZN ZN A 401 1555 1555 2.39 LINK SG CYS A 259 ZN ZN A 401 1555 1555 2.27 LINK SG CYS A 280 ZN ZN A 401 1555 1555 2.32 LINK SG CYS A 283 ZN ZN A 401 1555 1555 2.33 CISPEP 1 GLU A 325 PRO A 326 0 -2.17 SITE 1 AC1 4 CYS A 256 CYS A 259 CYS A 280 CYS A 283 SITE 1 AC2 7 GLU A 181 PHE A 294 GLY A 295 HOH A 596 SITE 2 AC2 7 HOH A 600 LYS F 3 FDL F 4 SITE 1 AC3 2 GLN A 300 LEU A 304 SITE 1 AC4 20 TYR A 175 GLU A 177 PHE A 180 GLU A 181 SITE 2 AC4 20 HIS A 248 ILE A 291 VAL A 292 PHE A 293 SITE 3 AC4 20 PHE A 294 GLY A 295 GLU A 296 PRO A 297 SITE 4 AC4 20 LEU A 298 GLU A 325 PRO A 326 PIT A 402 SITE 5 AC4 20 HOH A 564 HOH F 101 HOH F 102 HOH F 103 CRYST1 114.600 114.600 123.700 90.00 90.00 120.00 H 3 2 18 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 0.008726 0.005038 0.000000 0.00000 SCALE2 0.000000 0.010076 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008084 0.00000