HEADER TRANSCRIPTION 23-FEB-16 5ICN TITLE HDAC1:MTA1 IN COMPLEX WITH INOSITOL-6-PHOSPHATE AND A NOVEL PEPTIDE TITLE 2 INHIBITOR BASED ON HISTONE H4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METASTASIS-ASSOCIATED PROTEIN MTA1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HISTONE DEACETYLASE 1; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: HDAC1; COMPND 9 EC: 3.5.1.98; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: GLY-ALA-6A0-ARG-HIS; COMPND 13 CHAIN: C; COMPND 14 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: MTA1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 9 EXPRESSION_SYSTEM_ORGAN: KIDNEY; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCDNA3; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: HDAC1, RPD3L1; SOURCE 16 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 19 EXPRESSION_SYSTEM_ORGAN: KIDNEY; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PCDNA3; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 32630; SOURCE 25 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 26 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS TRANSCRIPTION REPRESSION INOSITOL PHOSPHATE COREPRESSOR HISTONE KEYWDS 2 DEACETYLASE HDAC1 HDAC3 HISTONES, TRANSCRIPTION, METASTASIS KEYWDS 3 ASSOCIATED PROTEIN, IP6 EXPDTA X-RAY DIFFRACTION AUTHOR C.J.MILLARD,N.S.ROBERTSON,P.J.WATSON,A.G.JAMESON,J.W.R.SCHWABE REVDAT 5 10-JAN-24 5ICN 1 LINK REVDAT 4 07-OCT-20 5ICN 1 COMPND REMARK HET HETNAM REVDAT 4 2 1 HETSYN LINK ATOM REVDAT 3 24-JAN-18 5ICN 1 SOURCE REVDAT 2 13-SEP-17 5ICN 1 REMARK REVDAT 1 11-MAY-16 5ICN 0 JRNL AUTH P.J.WATSON,C.J.MILLARD,A.M.RILEY,N.S.ROBERTSON,L.C.WRIGHT, JRNL AUTH 2 H.Y.GODAGE,S.M.COWLEY,A.G.JAMIESON,B.V.POTTER,J.W.SCHWABE JRNL TITL INSIGHTS INTO THE ACTIVATION MECHANISM OF CLASS I HDAC JRNL TITL 2 COMPLEXES BY INOSITOL PHOSPHATES. JRNL REF NAT COMMUN V. 7 11262 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27109927 JRNL DOI 10.1038/NCOMMS11262 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 93.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 12263 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) : 0.257 REMARK 3 R VALUE (WORKING SET) : 0.255 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 695 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 910 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.3500 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.4050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4326 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.93000 REMARK 3 B22 (A**2) : 0.93000 REMARK 3 B33 (A**2) : -3.02000 REMARK 3 B12 (A**2) : 0.47000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.617 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.643 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 41.500 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.835 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.759 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4466 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4066 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6050 ; 1.228 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9346 ; 0.760 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 538 ; 5.706 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 221 ;39.248 ;23.982 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 730 ;17.766 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;21.976 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 636 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5064 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1073 ; 0.001 ; 0.020 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): 2164 ; 1.420 ; 3.416 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2163 ; 1.421 ; 3.415 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2697 ; 2.456 ; 5.114 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2698 ; 2.456 ; 5.116 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2302 ; 1.311 ; 3.510 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2303 ; 1.310 ; 3.511 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3354 ; 2.322 ; 5.202 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5140 ; 4.252 ;26.672 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5141 ; 4.252 ;26.681 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 : NULL 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5ICN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218617. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 4 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96862 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.1.1 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13008 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 93.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.38000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.86000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: 4BKX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA HEPES PH7.5, 2M AMMONIUM REMARK 280 SULPHATE, 5% PEG400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 89.44067 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 44.72033 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 44.72033 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 89.44067 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -139.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 BIOMT1 2 -0.500000 0.866025 0.000000 -161.72250 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 93.37053 REMARK 350 BIOMT3 2 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 160 REMARK 465 ALA A 161 REMARK 465 ALA A 162 REMARK 465 ASP A 163 REMARK 465 LYS A 164 REMARK 465 CYS A 229 REMARK 465 SER A 230 REMARK 465 SER A 231 REMARK 465 SER A 232 REMARK 465 VAL A 233 REMARK 465 ARG A 234 REMARK 465 GLN A 235 REMARK 465 PRO A 236 REMARK 465 ARG A 341 REMARK 465 LEU A 342 REMARK 465 LYS A 343 REMARK 465 ALA A 344 REMARK 465 ALA A 345 REMARK 465 GLU A 346 REMARK 465 ALA A 347 REMARK 465 GLU A 348 REMARK 465 SER A 349 REMARK 465 LYS A 350 REMARK 465 LEU A 351 REMARK 465 LYS A 352 REMARK 465 GLN A 353 REMARK 465 VAL A 354 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLN B 3 REMARK 465 THR B 4 REMARK 465 GLN B 5 REMARK 465 GLY B 6 REMARK 465 THR B 7 REMARK 465 LEU C 10 REMARK 465 GLY C 11 REMARK 465 LYS C 12 REMARK 465 GLY C 13 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 182 CG CD CE NZ REMARK 470 GLU A 183 CG CD OE1 OE2 REMARK 470 GLU A 185 CG CD OE1 OE2 REMARK 470 ARG A 193 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 239 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 334 CG OD1 OD2 REMARK 470 ARG A 335 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 339 CG CD OE1 NE2 REMARK 470 LYS A 340 CG CD CE NZ REMARK 470 LYS B 74 CG CD CE NZ REMARK 470 ARG B 80 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 89 CG CD CE NZ REMARK 470 GLU B 108 CG CD OE1 OE2 REMARK 470 ASN B 349 CG OD1 ND2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PHE B 287 OG SER B 290 2.19 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 TYR A 173 -52.87 -129.01 REMARK 500 TRP A 199 119.15 -162.99 REMARK 500 LEU A 227 31.42 -86.34 REMARK 500 GLN A 275 42.45 -141.68 REMARK 500 LYS A 305 42.36 -96.95 REMARK 500 ASP B 82 -70.60 -66.66 REMARK 500 ASN B 83 35.61 -82.25 REMARK 500 SER B 88 -30.08 -38.66 REMARK 500 PHE B 150 -1.56 67.70 REMARK 500 CYS B 261 58.78 -104.47 REMARK 500 CYS B 273 47.45 -140.19 REMARK 500 ASN B 292 52.19 37.82 REMARK 500 ASP B 321 52.19 33.17 REMARK 500 ASN B 354 77.36 -107.53 REMARK 500 ALA C 15 -65.63 -124.62 REMARK 500 ARG C 17 74.02 -165.39 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 K B 402 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 174 O REMARK 620 2 ASP B 174 OD1 71.9 REMARK 620 3 ASP B 176 O 105.9 101.0 REMARK 620 4 HIS B 178 O 153.0 81.1 77.3 REMARK 620 5 SER B 197 OG 86.1 99.6 158.5 100.3 REMARK 620 6 PHE B 198 O 81.1 145.6 65.9 123.0 99.4 REMARK 620 N 1 2 3 4 5 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 ASP B 176 OD1 REMARK 620 2 HIS B 178 ND1 118.4 REMARK 620 3 ASP B 264 OD2 118.6 96.0 REMARK 620 4 6A0 C 16 O2 141.1 90.8 79.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 403 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 187 O REMARK 620 2 THR B 190 O 76.9 REMARK 620 3 VAL B 193 O 99.5 72.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IHP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 403 DBREF 5ICN A 162 354 UNP Q13330 MTA1_HUMAN 162 354 DBREF 5ICN B 1 376 UNP Q13547 HDAC1_HUMAN 1 376 DBREF 5ICN C 10 18 PDB 5ICN 5ICN 10 18 SEQADV 5ICN GLY A 160 UNP Q13330 EXPRESSION TAG SEQADV 5ICN ALA A 161 UNP Q13330 EXPRESSION TAG SEQRES 1 A 195 GLY ALA ALA ASP LYS GLY GLU ILE ARG VAL GLY ASN ARG SEQRES 2 A 195 TYR GLN ALA ASP ILE THR ASP LEU LEU LYS GLU GLY GLU SEQRES 3 A 195 GLU ASP GLY ARG ASP GLN SER ARG LEU GLU THR GLN VAL SEQRES 4 A 195 TRP GLU ALA HIS ASN PRO LEU THR ASP LYS GLN ILE ASP SEQRES 5 A 195 GLN PHE LEU VAL VAL ALA ARG SER VAL GLY THR PHE ALA SEQRES 6 A 195 ARG ALA LEU ASP CYS SER SER SER VAL ARG GLN PRO SER SEQRES 7 A 195 LEU HIS MET SER ALA ALA ALA ALA SER ARG ASP ILE THR SEQRES 8 A 195 LEU PHE HIS ALA MET ASP THR LEU HIS LYS ASN ILE TYR SEQRES 9 A 195 ASP ILE SER LYS ALA ILE SER ALA LEU VAL PRO GLN GLY SEQRES 10 A 195 GLY PRO VAL LEU CYS ARG ASP GLU MET GLU GLU TRP SER SEQRES 11 A 195 ALA SER GLU ALA ASN LEU PHE GLU GLU ALA LEU GLU LYS SEQRES 12 A 195 TYR GLY LYS ASP PHE THR ASP ILE GLN GLN ASP PHE LEU SEQRES 13 A 195 PRO TRP LYS SER LEU THR SER ILE ILE GLU TYR TYR TYR SEQRES 14 A 195 MET TRP LYS THR THR ASP ARG TYR VAL GLN GLN LYS ARG SEQRES 15 A 195 LEU LYS ALA ALA GLU ALA GLU SER LYS LEU LYS GLN VAL SEQRES 1 B 376 MET ALA GLN THR GLN GLY THR ARG ARG LYS VAL CYS TYR SEQRES 2 B 376 TYR TYR ASP GLY ASP VAL GLY ASN TYR TYR TYR GLY GLN SEQRES 3 B 376 GLY HIS PRO MET LYS PRO HIS ARG ILE ARG MET THR HIS SEQRES 4 B 376 ASN LEU LEU LEU ASN TYR GLY LEU TYR ARG LYS MET GLU SEQRES 5 B 376 ILE TYR ARG PRO HIS LYS ALA ASN ALA GLU GLU MET THR SEQRES 6 B 376 LYS TYR HIS SER ASP ASP TYR ILE LYS PHE LEU ARG SER SEQRES 7 B 376 ILE ARG PRO ASP ASN MET SER GLU TYR SER LYS GLN MET SEQRES 8 B 376 GLN ARG PHE ASN VAL GLY GLU ASP CYS PRO VAL PHE ASP SEQRES 9 B 376 GLY LEU PHE GLU PHE CYS GLN LEU SER THR GLY GLY SER SEQRES 10 B 376 VAL ALA SER ALA VAL LYS LEU ASN LYS GLN GLN THR ASP SEQRES 11 B 376 ILE ALA VAL ASN TRP ALA GLY GLY LEU HIS HIS ALA LYS SEQRES 12 B 376 LYS SER GLU ALA SER GLY PHE CYS TYR VAL ASN ASP ILE SEQRES 13 B 376 VAL LEU ALA ILE LEU GLU LEU LEU LYS TYR HIS GLN ARG SEQRES 14 B 376 VAL LEU TYR ILE ASP ILE ASP ILE HIS HIS GLY ASP GLY SEQRES 15 B 376 VAL GLU GLU ALA PHE TYR THR THR ASP ARG VAL MET THR SEQRES 16 B 376 VAL SER PHE HIS LYS TYR GLY GLU TYR PHE PRO GLY THR SEQRES 17 B 376 GLY ASP LEU ARG ASP ILE GLY ALA GLY LYS GLY LYS TYR SEQRES 18 B 376 TYR ALA VAL ASN TYR PRO LEU ARG ASP GLY ILE ASP ASP SEQRES 19 B 376 GLU SER TYR GLU ALA ILE PHE LYS PRO VAL MET SER LYS SEQRES 20 B 376 VAL MET GLU MET PHE GLN PRO SER ALA VAL VAL LEU GLN SEQRES 21 B 376 CYS GLY SER ASP SER LEU SER GLY ASP ARG LEU GLY CYS SEQRES 22 B 376 PHE ASN LEU THR ILE LYS GLY HIS ALA LYS CYS VAL GLU SEQRES 23 B 376 PHE VAL LYS SER PHE ASN LEU PRO MET LEU MET LEU GLY SEQRES 24 B 376 GLY GLY GLY TYR THR ILE ARG ASN VAL ALA ARG CYS TRP SEQRES 25 B 376 THR TYR GLU THR ALA VAL ALA LEU ASP THR GLU ILE PRO SEQRES 26 B 376 ASN GLU LEU PRO TYR ASN ASP TYR PHE GLU TYR PHE GLY SEQRES 27 B 376 PRO ASP PHE LYS LEU HIS ILE SER PRO SER ASN MET THR SEQRES 28 B 376 ASN GLN ASN THR ASN GLU TYR LEU GLU LYS ILE LYS GLN SEQRES 29 B 376 ARG LEU PHE GLU ASN LEU ARG MET LEU PRO HIS ALA SEQRES 1 C 9 LEU GLY LYS GLY GLY ALA 6A0 ARG HIS HET 6A0 C 16 13 HET IHP A 401 36 HET ZN B 401 1 HET K B 402 1 HET K B 403 1 HETNAM 6A0 (2S)-2-AMINO-8-(HYDROXYAMINO)-8-OXOOCTANOIC ACID HETNAM IHP INOSITOL HEXAKISPHOSPHATE HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETSYN IHP MYO-INOSITOL HEXAKISPHOSPHATE; INOSITOL 1,2,3,4,5,6- HETSYN 2 IHP HEXAKISPHOSPHATE FORMUL 3 6A0 C8 H16 N2 O4 FORMUL 4 IHP C6 H18 O24 P6 FORMUL 5 ZN ZN 2+ FORMUL 6 K 2(K 1+) HELIX 1 AA1 ASP A 190 ARG A 193 5 4 HELIX 2 AA2 THR A 206 LEU A 227 1 22 HELIX 3 AA3 LEU A 238 SER A 246 1 9 HELIX 4 AA4 ARG A 247 ASN A 261 1 15 HELIX 5 AA5 ASP A 264 VAL A 273 1 10 HELIX 6 AA6 ASP A 283 TRP A 288 1 6 HELIX 7 AA7 SER A 289 GLY A 304 1 16 HELIX 8 AA8 ASP A 306 PHE A 314 1 9 HELIX 9 AA9 SER A 319 LYS A 331 1 13 HELIX 10 AB1 ASP B 16 ASN B 21 5 6 HELIX 11 AB2 PRO B 32 TYR B 45 1 14 HELIX 12 AB3 LEU B 47 MET B 51 5 5 HELIX 13 AB4 ASN B 60 THR B 65 1 6 HELIX 14 AB5 SER B 69 ILE B 79 1 11 HELIX 15 AB6 ASN B 83 PHE B 94 1 12 HELIX 16 AB7 GLY B 105 LYS B 126 1 22 HELIX 17 AB8 ASN B 154 LEU B 164 1 11 HELIX 18 AB9 GLY B 180 PHE B 187 1 8 HELIX 19 AC1 ALA B 216 LYS B 220 5 5 HELIX 20 AC2 ASP B 233 GLN B 253 1 21 HELIX 21 AC3 THR B 277 PHE B 291 1 15 HELIX 22 AC4 THR B 304 LEU B 320 1 17 HELIX 23 AC5 TYR B 333 PHE B 337 5 5 HELIX 24 AC6 THR B 355 MET B 372 1 18 SHEET 1 AA1 9 GLU A 195 TRP A 199 0 SHEET 2 AA1 9 GLU B 52 PRO B 56 -1 O ILE B 53 N VAL A 198 SHEET 3 AA1 9 VAL B 11 TYR B 14 1 N TYR B 13 O TYR B 54 SHEET 4 AA1 9 ILE B 131 ASN B 134 1 O VAL B 133 N CYS B 12 SHEET 5 AA1 9 MET B 295 LEU B 298 1 O MET B 297 N ASN B 134 SHEET 6 AA1 9 ALA B 256 GLN B 260 1 N LEU B 259 O LEU B 298 SHEET 7 AA1 9 VAL B 170 ASP B 174 1 N ILE B 173 O GLN B 260 SHEET 8 AA1 9 VAL B 193 LYS B 200 1 O MET B 194 N TYR B 172 SHEET 9 AA1 9 ALA B 223 LEU B 228 1 O TYR B 226 N SER B 197 LINK C ALA C 15 N 6A0 C 16 1555 1555 1.34 LINK C 6A0 C 16 N ARG C 17 1555 1555 1.34 LINK O ASP B 174 K K B 402 1555 1555 3.00 LINK OD1 ASP B 174 K K B 402 1555 1555 2.56 LINK OD1 ASP B 176 ZN ZN B 401 1555 1555 1.95 LINK O ASP B 176 K K B 402 1555 1555 2.45 LINK ND1 HIS B 178 ZN ZN B 401 1555 1555 2.11 LINK O HIS B 178 K K B 402 1555 1555 3.18 LINK O PHE B 187 K K B 403 1555 1555 2.77 LINK O THR B 190 K K B 403 1555 1555 3.27 LINK O VAL B 193 K K B 403 1555 1555 3.15 LINK OG SER B 197 K K B 402 1555 1555 2.89 LINK O PHE B 198 K K B 402 1555 1555 3.07 LINK OD2 ASP B 264 ZN ZN B 401 1555 1555 1.93 LINK ZN ZN B 401 O2 6A0 C 16 1555 1555 2.35 CISPEP 1 PHE B 205 PRO B 206 0 4.61 SITE 1 AC1 8 LYS A 305 TYR A 327 TYR A 328 LYS A 331 SITE 2 AC1 8 GLY B 27 LYS B 31 ARG B 270 ILE B 305 SITE 1 AC2 4 ASP B 176 HIS B 178 ASP B 264 6A0 C 16 SITE 1 AC3 5 ASP B 174 ASP B 176 HIS B 178 SER B 197 SITE 2 AC3 5 PHE B 198 SITE 1 AC4 4 PHE B 187 THR B 190 VAL B 193 TYR B 222 CRYST1 107.815 107.815 134.161 90.00 90.00 120.00 P 32 2 1 6 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 0.009275 0.005355 0.000000 0.00000 SCALE2 0.000000 0.010710 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007454 0.00000