PDB Short entry for 2VQM HEADER HYDROLASE 17-MAR-08 2VQM TITLE STRUCTURE OF HDAC4 CATALYTIC DOMAIN BOUND TO A HYDROXAMIC ACID TITLE 2 INHBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 648-1057; COMPND 5 SYNONYM: HD4; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETM-11 (OBTAINED FROM EMBL-HEIDELBERG) KEYWDS INHIBITOR, REPRESSOR, CHROMATIN, COILED COIL, HISTONE DEACETYLASE, KEYWDS 2 TRANSCRIPTION REGULATION, UBL CONJUGATION, CHROMATIN REGULATOR, KEYWDS 3 POLYMORPHISM, TRANSCRIPTION, PHOSPHOPROTEIN, HDAC, ZINC, HDACI, KEYWDS 4 NUCLEUS, HYDROLASE, CYTOPLASM EXPDTA X-RAY DIFFRACTION AUTHOR M.J.BOTTOMLEY,P.LO SURDO,P.DI GIOVINE,A.CIRILLO,R.SCARPELLI, AUTHOR 2 F.FERRIGNO,P.JONES,P.NEDDERMANN,R.DE FRANCESCO,C.STEINKUHLER, AUTHOR 3 P.GALLINARI,A.CARFI REVDAT 4 13-DEC-23 2VQM 1 LINK REVDAT 3 24-FEB-09 2VQM 1 VERSN REVDAT 2 30-SEP-08 2VQM 1 JRNL REVDAT 1 08-JUL-08 2VQM 0 JRNL AUTH M.J.BOTTOMLEY,P.LO SURDO,P.DI GIOVINE,A.CIRILLO,R.SCARPELLI, JRNL AUTH 2 F.FERRIGNO,P.JONES,P.NEDDERMANN,R.DE FRANCESCO, JRNL AUTH 3 C.STEINKUHLER,P.GALLINARI,A.CARFI JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF THE HUMAN HDAC4 JRNL TITL 2 CATALYTIC DOMAIN REVEALS A REGULATORY ZINC-BINDING DOMAIN. JRNL REF J.BIOL.CHEM. V. 283 26694 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18614528 JRNL DOI 10.1074/JBC.M803514200 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 46272 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2494 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3388 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE SET COUNT : 174 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2940 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.76000 REMARK 3 B22 (A**2) : -0.60000 REMARK 3 B33 (A**2) : -1.16000 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): 0.128 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.975 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3030 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2009 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4112 ; 1.389 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4874 ; 1.011 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 388 ; 6.085 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 127 ;32.921 ;23.701 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 474 ;15.399 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;18.799 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 458 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3429 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 608 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 671 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2004 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1432 ; 0.171 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1452 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 201 ; 0.206 ; 0.200 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): 19 ; 0.288 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 43 ; 0.248 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.275 ; 0.200 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): 1928 ; 0.675 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3078 ; 1.232 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1112 ; 1.765 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1034 ; 2.783 ; 4.500 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 : 1.40 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. REMARK 4 REMARK 4 2VQM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1290035716. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.94 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48786 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 70.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 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 2VQJ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M AMMONIUM SULPHATE 0.1M MES PH 6.4 REMARK 280 10% DIOXANE 1MM DTT REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.80150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.80150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 54.43300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 69.10400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 54.43300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 69.10400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 34.80150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 54.43300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.10400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 34.80150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 54.43300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 69.10400 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 1 REMARK 465 ALA A 2 REMARK 465 MET A 3 REMARK 465 THR A 4 REMARK 465 LYS A 5 REMARK 465 SER A 27 REMARK 465 SER A 28 REMARK 465 SER A 29 REMARK 465 SER A 30 REMARK 465 HIS A 31 REMARK 465 PRO A 32 REMARK 465 GLU A 33 REMARK 465 LYS A 88 REMARK 465 LEU A 89 REMARK 465 ASP A 90 REMARK 465 SER A 91 REMARK 465 GLU A 408 REMARK 465 ALA A 409 REMARK 465 GLU A 410 REMARK 465 THR A 411 REMARK 465 VAL A 412 REMARK 465 THR A 413 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 PRO A 6 CB CG CD REMARK 470 LYS A 93 CG CD CE NZ REMARK 470 ARG A 389 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 407 CG CD OE1 OE2 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 SD MET A 317 O HOH A 2306 2.13 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 2139 O HOH A 2339 6545 1.89 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 THR A 297 N - CA - C ANGL. DEV. = 18.8 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 ALA A 35 114.89 60.20 REMARK 500 LEU A 254 52.08 -113.14 REMARK 500 ALA A 279 63.30 61.89 REMARK 500 SER A 287 73.77 -100.80 REMARK 500 THR A 297 -40.13 16.06 REMARK 500 GLU A 329 -110.91 -112.75 REMARK 500 HIS A 332 -49.27 -132.06 REMARK 500 ASN A 406 -75.31 -59.03 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 A2024 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2040 DISTANCE = 7.92 ANGSTROMS REMARK 525 HOH A2051 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A2095 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH A2160 DISTANCE = 6.40 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 A HYDROXAMIC ACID INHIBITOR (HAA): A HYDROXAMIC ACID REMARK 600 INHBITOR, SYNTHESIZED IN-HOUSE. 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 A1412 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 21 NE2 REMARK 620 2 CYS A 23 SG 112.3 REMARK 620 3 HIS A 34 NE2 108.7 99.3 REMARK 620 4 CYS A 107 SG 105.3 114.5 116.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1408 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 194 O REMARK 620 2 ASP A 194 OD1 68.0 REMARK 620 3 ASP A 196 O 99.6 98.1 REMARK 620 4 HIS A 198 O 163.1 95.3 79.7 REMARK 620 5 SER A 217 OG 81.1 112.2 147.1 108.7 REMARK 620 6 LEU A 218 O 73.3 135.0 66.4 120.7 82.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1411 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 196 OD2 REMARK 620 2 HIS A 198 ND1 101.1 REMARK 620 3 ASP A 290 OD2 106.1 96.5 REMARK 620 4 HA3 A1410 OAY 165.7 88.5 83.0 REMARK 620 5 HOH A2375 O 89.1 105.7 150.2 78.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1409 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 207 O REMARK 620 2 ASP A 210 O 72.9 REMARK 620 3 VAL A 213 O 116.0 69.7 REMARK 620 4 PHE A 244 O 165.5 119.0 77.4 REMARK 620 5 HOH A2235 O 88.0 95.2 144.3 83.0 REMARK 620 6 HOH A2236 O 68.7 141.4 124.1 99.6 88.2 REMARK 620 N 1 2 3 4 5 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A1408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A1409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HA3 A1410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1412 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VQW RELATED DB: PDB REMARK 900 STRUCTURE OF INHIBITOR-FREE HDAC4 CATALYTIC DOMAIN (WITH GAIN-OF- REMARK 900 FUNCTION MUTATION HIS332TYR) REMARK 900 RELATED ID: 2VQQ RELATED DB: PDB REMARK 900 STRUCTURE OF HDAC4 CATALYTIC DOMAIN (A DOUBLE CYSTEINE-TO-ALANINE REMARK 900 MUTANT) BOUND TO A TRIFLUOROMETHYLKETONE INHBITOR REMARK 900 RELATED ID: 2VQO RELATED DB: PDB REMARK 900 STRUCTURE OF HDAC4 CATALYTIC DOMAIN WITH A GAIN-OF-FUNCTION MUATION REMARK 900 BOUND TO A TRIFLUOROMETHYLKETONE INHBITOR REMARK 900 RELATED ID: 2VQV RELATED DB: PDB REMARK 900 STRUCTURE OF HDAC4 CATALYTIC DOMAIN WITH A GAIN-OF-FUNCTION MUATION REMARK 900 BOUND TO A HYDROXAMIC ACID INHIBITOR REMARK 900 RELATED ID: 2VQJ RELATED DB: PDB REMARK 900 STRUCTURE OF HDAC4 CATALYTIC DOMAIN BOUND TO A REMARK 900 TRIFLUOROMETHYLKETONE INHBITOR REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE IS LIKELY TO BE AN INTERMOLECULAR DISULPHIDE BOND REMARK 999 BETWEEN SG ATOMS OF CYS25 AND RESIDUE CYS56 OF THE REMARK 999 NEIGHBOURING MOLECULE. DBREF 2VQM A 1 3 PDB 2VQM 2VQM 1 3 DBREF 2VQM A 4 413 UNP P56524 HDAC4_HUMAN 648 1057 SEQRES 1 A 413 GLY ALA MET THR LYS PRO ARG PHE THR THR GLY LEU VAL SEQRES 2 A 413 TYR ASP THR LEU MET LEU LYS HIS GLN CYS THR CYS GLY SEQRES 3 A 413 SER SER SER SER HIS PRO GLU HIS ALA GLY ARG ILE GLN SEQRES 4 A 413 SER ILE TRP SER ARG LEU GLN GLU THR GLY LEU ARG GLY SEQRES 5 A 413 LYS CYS GLU CYS ILE ARG GLY ARG LYS ALA THR LEU GLU SEQRES 6 A 413 GLU LEU GLN THR VAL HIS SER GLU ALA HIS THR LEU LEU SEQRES 7 A 413 TYR GLY THR ASN PRO LEU ASN ARG GLN LYS LEU ASP SER SEQRES 8 A 413 LYS LYS LEU LEU GLY SER LEU ALA SER VAL PHE VAL ARG SEQRES 9 A 413 LEU PRO CYS GLY GLY VAL GLY VAL ASP SER ASP THR ILE SEQRES 10 A 413 TRP ASN GLU VAL HIS SER ALA GLY ALA ALA ARG LEU ALA SEQRES 11 A 413 VAL GLY CYS VAL VAL GLU LEU VAL PHE LYS VAL ALA THR SEQRES 12 A 413 GLY GLU LEU LYS ASN GLY PHE ALA VAL VAL ARG PRO PRO SEQRES 13 A 413 GLY HIS HIS ALA GLU GLU SER THR PRO MET GLY PHE CYS SEQRES 14 A 413 TYR PHE ASN SER VAL ALA VAL ALA ALA LYS LEU LEU GLN SEQRES 15 A 413 GLN ARG LEU SER VAL SER LYS ILE LEU ILE VAL ASP TRP SEQRES 16 A 413 ASP VAL HIS HIS GLY ASN GLY THR GLN GLN ALA PHE TYR SEQRES 17 A 413 SER ASP PRO SER VAL LEU TYR MET SER LEU HIS ARG TYR SEQRES 18 A 413 ASP ASP GLY ASN PHE PHE PRO GLY SER GLY ALA PRO ASP SEQRES 19 A 413 GLU VAL GLY THR GLY PRO GLY VAL GLY PHE ASN VAL ASN SEQRES 20 A 413 MET ALA PHE THR GLY GLY LEU ASP PRO PRO MET GLY ASP SEQRES 21 A 413 ALA GLU TYR LEU ALA ALA PHE ARG THR VAL VAL MET PRO SEQRES 22 A 413 ILE ALA SER GLU PHE ALA PRO ASP VAL VAL LEU VAL SER SEQRES 23 A 413 SER GLY PHE ASP ALA VAL GLU GLY HIS PRO THR PRO LEU SEQRES 24 A 413 GLY GLY TYR ASN LEU SER ALA ARG CYS PHE GLY TYR LEU SEQRES 25 A 413 THR LYS GLN LEU MET GLY LEU ALA GLY GLY ARG ILE VAL SEQRES 26 A 413 LEU ALA LEU GLU GLY GLY HIS ASP LEU THR ALA ILE CYS SEQRES 27 A 413 ASP ALA SER GLU ALA CYS VAL SER ALA LEU LEU GLY ASN SEQRES 28 A 413 GLU LEU ASP PRO LEU PRO GLU LYS VAL LEU GLN GLN ARG SEQRES 29 A 413 PRO ASN ALA ASN ALA VAL ARG SER MET GLU LYS VAL MET SEQRES 30 A 413 GLU ILE HIS SER LYS TYR TRP ARG CYS LEU GLN ARG THR SEQRES 31 A 413 THR SER THR ALA GLY ARG SER LEU ILE GLU ALA GLN THR SEQRES 32 A 413 CYS GLU ASN GLU GLU ALA GLU THR VAL THR HET K A1408 1 HET K A1409 1 HET HA3 A1410 26 HET ZN A1411 1 HET ZN A1412 1 HETNAM K POTASSIUM ION HETNAM HA3 N-HYDROXY-5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2- HETNAM 2 HA3 A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHENE-2-CARBOXAMIDE HETNAM ZN ZINC ION FORMUL 2 K 2(K 1+) FORMUL 4 HA3 C18 H16 N4 O3 S FORMUL 5 ZN 2(ZN 2+) FORMUL 7 HOH *360(H2 O) HELIX 1 1 ASP A 15 LEU A 19 5 5 HELIX 2 2 GLY A 36 GLU A 47 1 12 HELIX 3 3 LEU A 50 CYS A 54 1 5 HELIX 4 4 THR A 63 GLN A 68 1 6 HELIX 5 5 GLU A 73 TYR A 79 1 7 HELIX 6 6 PRO A 83 GLN A 87 5 5 HELIX 7 7 LYS A 92 VAL A 101 1 10 HELIX 8 8 ILE A 117 THR A 143 1 27 HELIX 9 9 SER A 173 LEU A 185 1 13 HELIX 10 10 GLY A 200 TYR A 208 1 9 HELIX 11 12 THR A 238 VAL A 242 5 5 HELIX 12 13 GLY A 259 VAL A 270 1 12 HELIX 13 14 VAL A 270 ALA A 279 1 10 HELIX 14 15 SER A 305 GLY A 318 1 14 HELIX 15 17 ASP A 333 LEU A 349 1 17 HELIX 16 18 PRO A 357 GLN A 363 1 7 HELIX 17 19 ASN A 366 LYS A 382 1 17 HELIX 18 20 TRP A 384 GLN A 388 5 5 HELIX 19 21 SER A 397 CYS A 404 1 8 SHEET 1 AA 8 GLU A 55 ILE A 57 0 SHEET 2 AA 8 THR A 10 VAL A 13 1 O THR A 10 N GLU A 55 SHEET 3 AA 8 ASN A 148 ALA A 151 1 O ASN A 148 N GLY A 11 SHEET 4 AA 8 ILE A 324 LEU A 328 1 O ILE A 324 N GLY A 149 SHEET 5 AA 8 VAL A 282 SER A 287 1 O VAL A 283 N VAL A 325 SHEET 6 AA 8 ILE A 190 ASP A 194 1 O LEU A 191 N LEU A 284 SHEET 7 AA 8 VAL A 213 ARG A 220 1 O LEU A 214 N ILE A 192 SHEET 8 AA 8 ASN A 245 PHE A 250 1 O VAL A 246 N SER A 217 SHEET 1 AB 2 PHE A 102 ARG A 104 0 SHEET 2 AB 2 VAL A 110 VAL A 112 -1 O GLY A 111 N VAL A 103 SSBOND 1 CYS A 25 CYS A 56 1555 3555 2.43 LINK NE2 HIS A 21 ZN ZN A1412 1555 1555 2.16 LINK SG CYS A 23 ZN ZN A1412 1555 1555 2.42 LINK NE2 HIS A 34 ZN ZN A1412 1555 1555 1.90 LINK SG CYS A 107 ZN ZN A1412 1555 1555 2.25 LINK O ASP A 194 K K A1408 1555 1555 2.95 LINK OD1 ASP A 194 K K A1408 1555 1555 2.84 LINK O ASP A 196 K K A1408 1555 1555 2.64 LINK OD2 ASP A 196 ZN ZN A1411 1555 1555 2.06 LINK O HIS A 198 K K A1408 1555 1555 2.72 LINK ND1 HIS A 198 ZN ZN A1411 1555 1555 2.13 LINK O PHE A 207 K K A1409 1555 1555 2.68 LINK O ASP A 210 K K A1409 1555 1555 2.99 LINK O VAL A 213 K K A1409 1555 1555 2.81 LINK OG SER A 217 K K A1408 1555 1555 2.92 LINK O LEU A 218 K K A1408 1555 1555 2.81 LINK O PHE A 244 K K A1409 1555 1555 2.97 LINK OD2 ASP A 290 ZN ZN A1411 1555 1555 1.91 LINK K K A1409 O HOH A2235 1555 1555 2.76 LINK K K A1409 O HOH A2236 1555 1555 3.06 LINK OAY HA3 A1410 ZN ZN A1411 1555 1555 2.49 LINK ZN ZN A1411 O HOH A2375 1555 1555 2.04 CISPEP 1 ARG A 154 PRO A 155 0 -6.03 CISPEP 2 PHE A 227 PRO A 228 0 -3.40 CISPEP 3 ASP A 255 PRO A 256 0 -2.71 SITE 1 AC1 5 ASP A 194 ASP A 196 HIS A 198 SER A 217 SITE 2 AC1 5 LEU A 218 SITE 1 AC2 6 PHE A 207 ASP A 210 VAL A 213 PHE A 244 SITE 2 AC2 6 HOH A2235 HOH A2236 SITE 1 AC3 16 LEU A 78 TYR A 79 VAL A 121 ALA A 124 SITE 2 AC3 16 PRO A 156 GLY A 167 PHE A 168 HIS A 198 SITE 3 AC3 16 PHE A 227 ASP A 290 GLY A 330 ZN A1411 SITE 4 AC3 16 HOH A2296 HOH A2372 HOH A2373 HOH A2375 SITE 1 AC4 5 ASP A 196 HIS A 198 ASP A 290 HA3 A1410 SITE 2 AC4 5 HOH A2375 SITE 1 AC5 4 HIS A 21 CYS A 23 HIS A 34 CYS A 107 CRYST1 108.866 138.208 69.603 90.00 90.00 90.00 C 2 2 21 8 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 0.009186 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007235 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014367 0.00000