HEADER IMMUNE SYSTEM 07-FEB-12 4DMB TITLE X-RAY STRUCTURE OF HUMAN HEPATITUS C VIRUS NS5A-TRANSACTIVATED PROTEIN TITLE 2 2 AT THE RESOLUTION 1.9A, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TITLE 3 (NESG) TARGET HR6723 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HD DOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HEPATITIS C VIRUS NS5A-TRANSACTIVATED PROTEIN 2, HCV NS5A- COMPND 5 TRANSACTIVATED PROTEIN 2; 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 STRAIN: BL21(DE3)+ MAGIC; SOURCE 6 GENE: HDDC2, C6ORF74, NS5ATP2, CGI-130; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), HD DOMAIN- KEYWDS 3 CONTAINING PROTEIN 2, HEPATITUS C VIRUS NS5A-TRANSACTIVATED PROTEIN KEYWDS 4 2, HCV NS5A-TRANSACTIVATED PROTEIN 2, MITOCHONDRIAL PROTEIN KEYWDS 5 PARTNERSHIP, MPP, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.KUZIN,M.SU,J.SEETHARAMAN,P.PATEL,R.XIAO,C.CICCOSANTI,D.LEE, AUTHOR 2 J.K.EVERETT,T.B.ACTON,G.T.MONTELIONE,J.F.HUNT,L.TONG,NORTHEAST AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (NESG),MITOCHONDRIAL PROTEIN AUTHOR 4 PARTNERSHIP (MPP) REVDAT 2 11-APR-12 4DMB 1 KEYWDS REVDAT 1 04-APR-12 4DMB 0 JRNL AUTH A.KUZIN,M.SU,J.SEETHARAMAN,P.PATEL,R.XIAO,C.CICCOSANTI, JRNL AUTH 2 D.LEE,J.K.EVERETT,T.B.ACTON,G.T.MONTELIONE,J.F.HUNT,L.TONG JRNL TITL NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR6723 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_988) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 32955 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1673 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 42.3058 - 4.3464 1.00 2897 142 0.2099 0.2059 REMARK 3 2 4.3464 - 3.4504 0.99 2713 137 0.1638 0.1885 REMARK 3 3 3.4504 - 3.0144 0.99 2651 151 0.1710 0.2038 REMARK 3 4 3.0144 - 2.7388 1.00 2627 157 0.1735 0.2408 REMARK 3 5 2.7388 - 2.5425 1.00 2639 139 0.1582 0.1737 REMARK 3 6 2.5425 - 2.3926 0.99 2623 149 0.1611 0.2066 REMARK 3 7 2.3926 - 2.2728 1.00 2637 132 0.1548 0.1971 REMARK 3 8 2.2728 - 2.1739 1.00 2646 130 0.1592 0.1889 REMARK 3 9 2.1739 - 2.0902 1.00 2585 144 0.1598 0.2019 REMARK 3 10 2.0902 - 2.0181 1.00 2603 134 0.1642 0.2210 REMARK 3 11 2.0181 - 1.9550 0.98 2529 139 0.1861 0.2403 REMARK 3 12 1.9550 - 1.8991 0.82 2132 119 0.2355 0.3152 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 39.58 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.420 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) : -0.75130 REMARK 3 B22 (A**2) : -0.75130 REMARK 3 B33 (A**2) : 1.50270 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 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 : 0.007 3228 REMARK 3 ANGLE : 0.988 4354 REMARK 3 CHIRALITY : 0.069 467 REMARK 3 PLANARITY : 0.004 574 REMARK 3 DIHEDRAL : 13.385 1283 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: all REMARK 3 ORIGIN FOR THE GROUP (A): 34.7794 53.7885 66.0152 REMARK 3 T TENSOR REMARK 3 T11: 0.1214 T22: 0.1387 REMARK 3 T33: 0.1717 T12: -0.0064 REMARK 3 T13: 0.0116 T23: 0.0065 REMARK 3 L TENSOR REMARK 3 L11: 0.4801 L22: 0.5664 REMARK 3 L33: 0.8907 L12: -0.1309 REMARK 3 L13: -0.1375 L23: 0.2878 REMARK 3 S TENSOR REMARK 3 S11: 0.0115 S12: -0.0029 S13: 0.0099 REMARK 3 S21: 0.0039 S22: -0.0167 S23: 0.0331 REMARK 3 S31: -0.0043 S32: -0.0391 S33: 0.0052 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 4DMB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-12. REMARK 100 THE RCSB ID CODE IS RCSB070508. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97906 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59948 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 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) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.45500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX.AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 100MM NACL, 5MM DTT, REMARK 280 0.02% NAN3, 10MM TRIS-HCL (PH 7.5) . RESERVOIR SOLUTION:MG(NO3)2 REMARK 280 0.1M, MES 0.1M, PEG4000 40% (W/V), MICROBATCH UNDER OIL, REMARK 280 TEMPERATURE 293KK REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 87.22600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.19650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.19650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 130.83900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.19650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.19650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.61300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.19650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.19650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 130.83900 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.19650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.19650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.61300 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 87.22600 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 300 REMARK: DIMER, OR TRIMER,61.41 KD,74.7%, OR HEPTAMER,138.4 KD,19.4% 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: 4910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 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 MSE A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 VAL A 4 REMARK 465 SER A 5 REMARK 465 SER A 6 REMARK 465 ALA A 7 REMARK 465 THR A 8 REMARK 465 PHE A 9 REMARK 465 SER A 10 REMARK 465 GLY A 11 REMARK 465 HIS A 12 REMARK 465 GLU A 201 REMARK 465 PRO A 202 REMARK 465 HIS A 203 REMARK 465 SER A 204 REMARK 465 MSE B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 VAL B 4 REMARK 465 SER B 5 REMARK 465 SER B 6 REMARK 465 ALA B 7 REMARK 465 THR B 8 REMARK 465 PHE B 9 REMARK 465 SER B 10 REMARK 465 GLU B 201 REMARK 465 PRO B 202 REMARK 465 HIS B 203 REMARK 465 SER B 204 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 62 96.69 -171.57 REMARK 500 ASN A 176 -12.52 -146.84 REMARK 500 ASP B 62 99.47 -171.65 REMARK 500 ASN B 176 -12.11 -143.58 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 MG B 305 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 480 O REMARK 620 2 ASP B 143 OD1 85.7 REMARK 620 3 ASP B 78 OD2 94.2 175.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 306 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 143 OD1 REMARK 620 2 ASP A 78 OD2 179.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 306 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 81 OE2 REMARK 620 2 ASP B 86 OD1 93.1 REMARK 620 3 HOH B 403 O 90.9 172.8 REMARK 620 4 HOH B 402 O 92.7 87.6 86.3 REMARK 620 5 HOH B 477 O 176.0 89.9 85.9 84.8 REMARK 620 6 HOH B 401 O 85.1 87.6 98.7 174.6 97.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 307 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 81 OE2 REMARK 620 2 ASP A 86 OD1 99.8 REMARK 620 3 HOH A 417 O 86.2 85.3 REMARK 620 4 HOH A 460 O 88.6 170.1 90.1 REMARK 620 5 HOH A 405 O 86.2 88.0 168.8 97.8 REMARK 620 6 HOH A 484 O 169.6 90.4 97.2 81.6 91.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CQZ RELATED DB: PDB REMARK 900 36.05% ID 69.12% SEQUENCE LENGTH E-VALUE: 3E-20 REMARK 900 RELATED ID: NESG-HR6723 RELATED DB: TARGETTRACK DBREF 4DMB A 1 204 UNP Q7Z4H3 HDDC2_HUMAN 1 204 DBREF 4DMB B 1 204 UNP Q7Z4H3 HDDC2_HUMAN 1 204 SEQRES 1 A 204 MSE ALA SER VAL SER SER ALA THR PHE SER GLY HIS GLY SEQRES 2 A 204 ALA ARG SER LEU LEU GLN PHE LEU ARG LEU VAL GLY GLN SEQRES 3 A 204 LEU LYS ARG VAL PRO ARG THR GLY TRP VAL TYR ARG ASN SEQRES 4 A 204 VAL GLN ARG PRO GLU SER VAL SER ASP HIS MSE TYR ARG SEQRES 5 A 204 MSE ALA VAL MSE ALA MSE VAL ILE LYS ASP ASP ARG LEU SEQRES 6 A 204 ASN LYS ASP ARG CYS VAL ARG LEU ALA LEU VAL HIS ASP SEQRES 7 A 204 MSE ALA GLU CYS ILE VAL GLY ASP ILE ALA PRO ALA ASP SEQRES 8 A 204 ASN ILE PRO LYS GLU GLU LYS HIS ARG ARG GLU GLU GLU SEQRES 9 A 204 ALA MSE LYS GLN ILE THR GLN LEU LEU PRO GLU ASP LEU SEQRES 10 A 204 ARG LYS GLU LEU TYR GLU LEU TRP GLU GLU TYR GLU THR SEQRES 11 A 204 GLN SER SER ALA GLU ALA LYS PHE VAL LYS GLN LEU ASP SEQRES 12 A 204 GLN CYS GLU MSE ILE LEU GLN ALA SER GLU TYR GLU ASP SEQRES 13 A 204 LEU GLU HIS LYS PRO GLY ARG LEU GLN ASP PHE TYR ASP SEQRES 14 A 204 SER THR ALA GLY LYS PHE ASN HIS PRO GLU ILE VAL GLN SEQRES 15 A 204 LEU VAL SER GLU LEU GLU ALA GLU ARG SER THR ASN ILE SEQRES 16 A 204 ALA ALA ALA ALA SER GLU PRO HIS SER SEQRES 1 B 204 MSE ALA SER VAL SER SER ALA THR PHE SER GLY HIS GLY SEQRES 2 B 204 ALA ARG SER LEU LEU GLN PHE LEU ARG LEU VAL GLY GLN SEQRES 3 B 204 LEU LYS ARG VAL PRO ARG THR GLY TRP VAL TYR ARG ASN SEQRES 4 B 204 VAL GLN ARG PRO GLU SER VAL SER ASP HIS MSE TYR ARG SEQRES 5 B 204 MSE ALA VAL MSE ALA MSE VAL ILE LYS ASP ASP ARG LEU SEQRES 6 B 204 ASN LYS ASP ARG CYS VAL ARG LEU ALA LEU VAL HIS ASP SEQRES 7 B 204 MSE ALA GLU CYS ILE VAL GLY ASP ILE ALA PRO ALA ASP SEQRES 8 B 204 ASN ILE PRO LYS GLU GLU LYS HIS ARG ARG GLU GLU GLU SEQRES 9 B 204 ALA MSE LYS GLN ILE THR GLN LEU LEU PRO GLU ASP LEU SEQRES 10 B 204 ARG LYS GLU LEU TYR GLU LEU TRP GLU GLU TYR GLU THR SEQRES 11 B 204 GLN SER SER ALA GLU ALA LYS PHE VAL LYS GLN LEU ASP SEQRES 12 B 204 GLN CYS GLU MSE ILE LEU GLN ALA SER GLU TYR GLU ASP SEQRES 13 B 204 LEU GLU HIS LYS PRO GLY ARG LEU GLN ASP PHE TYR ASP SEQRES 14 B 204 SER THR ALA GLY LYS PHE ASN HIS PRO GLU ILE VAL GLN SEQRES 15 B 204 LEU VAL SER GLU LEU GLU ALA GLU ARG SER THR ASN ILE SEQRES 16 B 204 ALA ALA ALA ALA SER GLU PRO HIS SER MODRES 4DMB MSE A 50 MET SELENOMETHIONINE MODRES 4DMB MSE A 53 MET SELENOMETHIONINE MODRES 4DMB MSE A 56 MET SELENOMETHIONINE MODRES 4DMB MSE A 58 MET SELENOMETHIONINE MODRES 4DMB MSE A 79 MET SELENOMETHIONINE MODRES 4DMB MSE A 106 MET SELENOMETHIONINE MODRES 4DMB MSE A 147 MET SELENOMETHIONINE MODRES 4DMB MSE B 50 MET SELENOMETHIONINE MODRES 4DMB MSE B 53 MET SELENOMETHIONINE MODRES 4DMB MSE B 56 MET SELENOMETHIONINE MODRES 4DMB MSE B 58 MET SELENOMETHIONINE MODRES 4DMB MSE B 79 MET SELENOMETHIONINE MODRES 4DMB MSE B 106 MET SELENOMETHIONINE MODRES 4DMB MSE B 147 MET SELENOMETHIONINE HET MSE A 50 8 HET MSE A 53 8 HET MSE A 56 8 HET MSE A 58 8 HET MSE A 79 8 HET MSE A 106 8 HET MSE A 147 13 HET MSE B 50 8 HET MSE B 53 8 HET MSE B 56 8 HET MSE B 58 8 HET MSE B 79 8 HET MSE B 106 8 HET MSE B 147 13 HET NO3 A 301 4 HET MG A 306 1 HET NO3 A 302 4 HET MG A 307 1 HET GOL A 303 12 HET PO4 A 304 5 HET PEG A 305 7 HET NO3 B 301 4 HET PO4 B 302 5 HET PEG B 303 7 HET UNL B 304 4 HET MG B 305 1 HET MG B 306 1 HETNAM MSE SELENOMETHIONINE HETNAM NO3 NITRATE ION HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM UNL UNKNOWN LIGAND HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 14(C5 H11 N O2 SE) FORMUL 3 NO3 3(N O3 1-) FORMUL 4 MG 4(MG 2+) FORMUL 7 GOL C3 H8 O3 FORMUL 8 PO4 2(O4 P 3-) FORMUL 9 PEG 2(C4 H10 O3) FORMUL 16 HOH *172(H2 O) HELIX 1 1 GLY A 13 LEU A 27 1 15 HELIX 2 2 ARG A 32 ARG A 38 1 7 HELIX 3 3 SER A 45 ILE A 60 1 16 HELIX 4 4 ASN A 66 HIS A 77 1 12 HELIX 5 5 ALA A 80 GLY A 85 1 6 HELIX 6 6 ALA A 88 ASN A 92 5 5 HELIX 7 7 PRO A 94 GLN A 111 1 18 HELIX 8 8 PRO A 114 GLN A 131 1 18 HELIX 9 9 SER A 133 HIS A 159 1 27 HELIX 10 10 LEU A 164 THR A 171 1 8 HELIX 11 11 HIS A 177 SER A 200 1 24 HELIX 12 12 HIS B 12 GLN B 26 1 15 HELIX 13 13 LEU B 27 ARG B 29 5 3 HELIX 14 14 ARG B 32 ARG B 38 1 7 HELIX 15 15 SER B 45 ILE B 60 1 16 HELIX 16 16 ASN B 66 HIS B 77 1 12 HELIX 17 17 ALA B 80 GLY B 85 1 6 HELIX 18 18 ALA B 88 ASN B 92 5 5 HELIX 19 19 PRO B 94 GLN B 111 1 18 HELIX 20 20 PRO B 114 GLN B 131 1 18 HELIX 21 21 SER B 133 HIS B 159 1 27 HELIX 22 22 LEU B 164 SER B 170 1 7 HELIX 23 23 HIS B 177 SER B 200 1 24 LINK C HIS A 49 N MSE A 50 1555 1555 1.33 LINK C MSE A 50 N TYR A 51 1555 1555 1.33 LINK C ARG A 52 N MSE A 53 1555 1555 1.33 LINK C MSE A 53 N ALA A 54 1555 1555 1.33 LINK C VAL A 55 N MSE A 56 1555 1555 1.33 LINK C MSE A 56 N ALA A 57 1555 1555 1.33 LINK C ALA A 57 N MSE A 58 1555 1555 1.33 LINK C MSE A 58 N VAL A 59 1555 1555 1.33 LINK C ASP A 78 N MSE A 79 1555 1555 1.33 LINK C MSE A 79 N ALA A 80 1555 1555 1.33 LINK C ALA A 105 N MSE A 106 1555 1555 1.33 LINK C MSE A 106 N LYS A 107 1555 1555 1.32 LINK C GLU A 146 N MSE A 147 1555 1555 1.32 LINK C MSE A 147 N ILE A 148 1555 1555 1.33 LINK C HIS B 49 N MSE B 50 1555 1555 1.33 LINK C MSE B 50 N TYR B 51 1555 1555 1.33 LINK C ARG B 52 N MSE B 53 1555 1555 1.33 LINK C MSE B 53 N ALA B 54 1555 1555 1.33 LINK C VAL B 55 N MSE B 56 1555 1555 1.33 LINK C MSE B 56 N ALA B 57 1555 1555 1.33 LINK C ALA B 57 N MSE B 58 1555 1555 1.33 LINK C MSE B 58 N VAL B 59 1555 1555 1.33 LINK C ASP B 78 N MSE B 79 1555 1555 1.33 LINK C MSE B 79 N ALA B 80 1555 1555 1.33 LINK C ALA B 105 N MSE B 106 1555 1555 1.34 LINK C MSE B 106 N LYS B 107 1555 1555 1.33 LINK C GLU B 146 N MSE B 147 1555 1555 1.32 LINK C MSE B 147 N ILE B 148 1555 1555 1.34 LINK MG MG B 305 O HOH B 480 1555 1555 1.96 LINK OD1 ASP A 143 MG MG A 306 1555 1555 1.98 LINK OD1 ASP B 143 MG MG B 305 1555 1555 2.01 LINK OE2 GLU B 81 MG MG B 306 1555 1555 2.04 LINK OE2 GLU A 81 MG MG A 307 1555 1555 2.09 LINK OD1 ASP A 86 MG MG A 307 1555 1555 2.11 LINK MG MG A 307 O HOH A 417 1555 1555 2.12 LINK OD1 ASP B 86 MG MG B 306 1555 1555 2.14 LINK MG MG B 306 O HOH B 403 1555 1555 2.17 LINK MG MG A 307 O HOH A 460 1555 1555 2.18 LINK MG MG B 306 O HOH B 402 1555 1555 2.19 LINK MG MG B 306 O HOH B 477 1555 1555 2.19 LINK OD2 ASP A 78 MG MG A 306 1555 1555 2.22 LINK MG MG B 306 O HOH B 401 1555 1555 2.23 LINK MG MG A 307 O HOH A 405 1555 1555 2.23 LINK MG MG A 307 O HOH A 484 1555 1555 2.28 LINK OD2 ASP B 78 MG MG B 305 1555 1555 2.34 SITE 1 AC1 3 ASP A 68 ARG A 69 ARG A 72 SITE 1 AC2 2 ASN A 66 HOH A 418 SITE 1 AC3 13 PRO A 43 GLU A 44 SER A 45 ASP A 48 SITE 2 AC3 13 HOH A 430 HOH A 483 HOH A 485 HOH A 486 SITE 3 AC3 13 HOH A 487 LYS B 28 PRO B 43 GLU B 44 SITE 4 AC3 13 SER B 45 SITE 1 AC4 8 ARG A 32 THR A 33 GLY A 34 TRP A 35 SITE 2 AC4 8 ASP A 86 MSE A 147 PHE A 167 HOH A 488 SITE 1 AC5 6 GLN A 165 TYR A 168 ASP A 169 ARG A 191 SITE 2 AC5 6 SER A 192 HOH A 411 SITE 1 AC6 4 HIS A 49 HIS A 77 ASP A 78 ASP A 143 SITE 1 AC7 6 GLU A 81 ASP A 86 HOH A 405 HOH A 417 SITE 2 AC7 6 HOH A 460 HOH A 484 SITE 1 AC8 3 ASP B 68 ARG B 69 ARG B 72 SITE 1 AC9 6 ALA B 57 ILE B 60 ASP B 62 LEU B 65 SITE 2 AC9 6 LYS B 67 HOH B 443 SITE 1 BC1 4 ARG B 29 VAL B 30 CYS B 82 ILE B 83 SITE 1 BC2 5 HIS B 49 HIS B 77 ASP B 78 ASP B 143 SITE 2 BC2 5 HOH B 480 SITE 1 BC3 6 GLU B 81 ASP B 86 HOH B 401 HOH B 402 SITE 2 BC3 6 HOH B 403 HOH B 477 CRYST1 68.393 68.393 174.452 90.00 90.00 90.00 P 43 21 2 16 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 0.014621 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014621 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005732 0.00000