HEADER HYDROLASE 30-SEP-16 5THU TITLE CRYSTAL STRUCTURE OF G304A HDAC8 IN COMPLEX WITH M344 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE 8; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HD8; COMPND 5 EC: 3.5.1.98; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HDAC8, HDACL1, CDA07; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET20B KEYWDS ZINC HISTONE DEACETYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.J.PORTER,D.W.CHRISTIANSON REVDAT 5 04-OCT-23 5THU 1 REMARK LINK REVDAT 4 25-DEC-19 5THU 1 REMARK REVDAT 3 18-APR-18 5THU 1 JRNL REVDAT 2 27-SEP-17 5THU 1 REMARK REVDAT 1 21-DEC-16 5THU 0 JRNL AUTH N.J.PORTER,N.H.CHRISTIANSON,C.DECROOS,D.W.CHRISTIANSON JRNL TITL STRUCTURAL AND FUNCTIONAL INFLUENCE OF THE GLYCINE-RICH LOOP JRNL TITL 2 G302GGGY ON THE CATALYTIC TYROSINE OF HISTONE DEACETYLASE 8. JRNL REF BIOCHEMISTRY V. 55 6718 2016 JRNL REFN ISSN 1520-4995 JRNL PMID 27933794 JRNL DOI 10.1021/ACS.BIOCHEM.6B01014 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 61982 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 : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190 REMARK 3 FREE R VALUE TEST SET COUNT : 3219 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 48.1696 - 5.5429 0.97 2553 153 0.1646 0.1575 REMARK 3 2 5.5429 - 4.4005 0.99 2549 149 0.1472 0.1761 REMARK 3 3 4.4005 - 3.8445 0.99 2586 121 0.1401 0.1538 REMARK 3 4 3.8445 - 3.4931 0.99 2542 160 0.1650 0.1828 REMARK 3 5 3.4931 - 3.2428 1.00 2565 143 0.1739 0.1951 REMARK 3 6 3.2428 - 3.0517 1.00 2562 157 0.1834 0.2328 REMARK 3 7 3.0517 - 2.8989 1.00 2533 147 0.1758 0.1946 REMARK 3 8 2.8989 - 2.7727 1.00 2555 150 0.1771 0.2070 REMARK 3 9 2.7727 - 2.6659 1.00 2529 140 0.1814 0.1882 REMARK 3 10 2.6659 - 2.5740 1.00 2574 137 0.1847 0.2217 REMARK 3 11 2.5740 - 2.4935 1.00 2523 164 0.1822 0.2147 REMARK 3 12 2.4935 - 2.4222 1.00 2552 150 0.1873 0.2303 REMARK 3 13 2.4222 - 2.3584 1.00 2578 139 0.1863 0.2290 REMARK 3 14 2.3584 - 2.3009 1.00 2545 128 0.1838 0.2179 REMARK 3 15 2.3009 - 2.2486 1.00 2583 121 0.2035 0.2477 REMARK 3 16 2.2486 - 2.2007 1.00 2566 122 0.2128 0.2311 REMARK 3 17 2.2007 - 2.1567 1.00 2533 132 0.1956 0.2206 REMARK 3 18 2.1567 - 2.1160 1.00 2595 117 0.1912 0.2440 REMARK 3 19 2.1160 - 2.0782 1.00 2538 148 0.1981 0.2238 REMARK 3 20 2.0782 - 2.0430 1.00 2535 140 0.2132 0.2745 REMARK 3 21 2.0430 - 2.0100 1.00 2602 115 0.2160 0.2662 REMARK 3 22 2.0100 - 1.9791 1.00 2511 144 0.2205 0.2420 REMARK 3 23 1.9791 - 1.9500 1.00 2554 142 0.2284 0.2777 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.420 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 5736 REMARK 3 ANGLE : 0.808 7796 REMARK 3 CHIRALITY : 0.052 851 REMARK 3 PLANARITY : 0.005 1004 REMARK 3 DIHEDRAL : 16.030 3366 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5THU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1000224267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.18076 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62024 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 52.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : 0.07700 REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3EWF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BISTRIS (PH 6.5), 10% W/V PEG REMARK 280 35000, 4 MM TCEP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 41.97500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 GLU A 3 REMARK 465 PRO A 4 REMARK 465 GLU A 5 REMARK 465 GLU A 6 REMARK 465 PRO A 7 REMARK 465 ALA A 8 REMARK 465 ASP A 9 REMARK 465 SER A 10 REMARK 465 GLY A 11 REMARK 465 GLN A 12 REMARK 465 SER A 13 REMARK 465 LEU A 31 REMARK 465 ALA A 32 REMARK 465 GLN A 84 REMARK 465 GLU A 85 REMARK 465 GLY A 86 REMARK 465 ASP A 87 REMARK 465 ASP A 88 REMARK 465 GLU A 379 REMARK 465 GLY A 380 REMARK 465 ARG A 381 REMARK 465 GLY A 382 REMARK 465 SER A 383 REMARK 465 HIS A 384 REMARK 465 HIS A 385 REMARK 465 HIS A 386 REMARK 465 HIS A 387 REMARK 465 HIS A 388 REMARK 465 HIS A 389 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLU B 3 REMARK 465 PRO B 4 REMARK 465 GLU B 5 REMARK 465 GLU B 6 REMARK 465 PRO B 7 REMARK 465 ALA B 8 REMARK 465 ASP B 9 REMARK 465 SER B 10 REMARK 465 GLY B 11 REMARK 465 GLN B 12 REMARK 465 SER B 13 REMARK 465 LEU B 31 REMARK 465 ALA B 32 REMARK 465 LYS B 33 REMARK 465 ILE B 34 REMARK 465 GLY B 86 REMARK 465 ASP B 87 REMARK 465 ASP B 88 REMARK 465 ASP B 89 REMARK 465 HIS B 90 REMARK 465 PRO B 91 REMARK 465 ASP B 92 REMARK 465 SER B 93 REMARK 465 ILE B 94 REMARK 465 GLU B 95 REMARK 465 GLY B 99 REMARK 465 TYR B 100 REMARK 465 ASP B 101 REMARK 465 CYS B 102 REMARK 465 PRO B 103 REMARK 465 ALA B 104 REMARK 465 ILE B 378 REMARK 465 GLU B 379 REMARK 465 GLY B 380 REMARK 465 ARG B 381 REMARK 465 GLY B 382 REMARK 465 SER B 383 REMARK 465 HIS B 384 REMARK 465 HIS B 385 REMARK 465 HIS B 386 REMARK 465 HIS B 387 REMARK 465 HIS B 388 REMARK 465 HIS B 389 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 36 CG CD CE NZ REMARK 470 LYS A 52 CD CE NZ REMARK 470 LYS A 60 CD CE NZ REMARK 470 ASP A 89 CG OD1 OD2 REMARK 470 LYS A 370 CE NZ REMARK 470 LYS A 374 CD CE NZ REMARK 470 LEU B 14 CG CD1 CD2 REMARK 470 LYS B 36 CD CE NZ REMARK 470 LYS B 52 CE NZ REMARK 470 LYS B 58 CD CE NZ REMARK 470 GLU B 65 CD OE1 OE2 REMARK 470 LYS B 81 CG CD CE NZ REMARK 470 LEU B 98 CG CD1 CD2 REMARK 470 LYS B 132 CG CD CE NZ REMARK 470 GLU B 238 CD OE1 OE2 REMARK 470 LYS B 258 CE NZ REMARK 470 LYS B 325 CE NZ REMARK 470 GLU B 358 CG CD OE1 OE2 REMARK 470 LYS B 370 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 33 CB CG CD CE NZ REMARK 480 GLU A 46 CD OE1 OE2 REMARK 480 GLU A 95 CG CD OE1 OE2 REMARK 480 TYR A 100 CB CG CD1 CD2 CE1 CE2 CZ REMARK 480 TYR A 100 OH REMARK 480 LYS A 325 CD CE NZ 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 PHE A 70 -50.67 -123.98 REMARK 500 TYR A 224 1.11 85.94 REMARK 500 TYR A 224 1.11 85.41 REMARK 500 SER A 276 -75.44 -112.67 REMARK 500 HIS A 334 -178.21 -175.91 REMARK 500 TYR B 224 4.23 83.13 REMARK 500 SER B 276 -75.93 -110.89 REMARK 500 HIS B 334 -174.28 -170.87 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 B 678 DISTANCE = 6.02 ANGSTROMS 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 A 402 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 176 O REMARK 620 2 ASP A 176 OD1 73.2 REMARK 620 3 ASP A 178 O 109.3 105.2 REMARK 620 4 HIS A 180 O 160.6 89.0 82.4 REMARK 620 5 SER A 199 OG 83.5 102.9 151.5 93.4 REMARK 620 6 LEU A 200 O 78.0 146.6 68.8 121.3 90.1 REMARK 620 N 1 2 3 4 5 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 ASP A 178 OD2 REMARK 620 2 HIS A 180 ND1 104.1 REMARK 620 3 ASP A 267 OD2 106.9 99.6 REMARK 620 4 B3N A 404 O4 87.3 100.3 151.8 REMARK 620 5 B3N A 404 O2 157.4 89.1 88.4 72.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 403 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 189 O REMARK 620 2 THR A 192 O 77.3 REMARK 620 3 VAL A 195 O 116.8 85.1 REMARK 620 4 TYR A 225 O 157.7 119.9 80.8 REMARK 620 5 HOH A 529 O 90.2 97.6 152.6 74.3 REMARK 620 6 HOH A 630 O 76.0 153.0 110.6 85.2 78.6 REMARK 620 N 1 2 3 4 5 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 176 O REMARK 620 2 ASP B 176 OD1 72.7 REMARK 620 3 ASP B 178 O 107.2 104.4 REMARK 620 4 HIS B 180 O 160.8 89.1 82.7 REMARK 620 5 SER B 199 OG 86.4 102.2 152.7 91.8 REMARK 620 6 LEU B 200 O 78.8 147.2 68.6 120.3 91.9 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 178 OD2 REMARK 620 2 HIS B 180 ND1 109.0 REMARK 620 3 ASP B 267 OD2 105.2 100.6 REMARK 620 4 B3N B 404 O2 153.5 88.7 90.1 REMARK 620 5 B3N B 404 O4 92.5 98.8 147.7 64.7 REMARK 620 N 1 2 3 4 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 189 O REMARK 620 2 THR B 192 O 78.5 REMARK 620 3 VAL B 195 O 112.4 83.2 REMARK 620 4 TYR B 225 O 160.0 118.9 81.2 REMARK 620 5 HOH B 526 O 92.0 96.2 154.7 77.0 REMARK 620 6 HOH B 611 O 73.5 151.6 111.5 88.1 80.7 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 ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B3N A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B3N B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GGG B 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5THS RELATED DB: PDB REMARK 900 RELATED ID: 5THT RELATED DB: PDB REMARK 900 RELATED ID: 5THV RELATED DB: PDB DBREF 5THU A 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 DBREF 5THU B 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 SEQADV 5THU ALA A 304 UNP Q9BY41 GLY 304 ENGINEERED MUTATION SEQADV 5THU ILE A 378 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU GLU A 379 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU GLY A 380 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU ARG A 381 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU GLY A 382 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU SER A 383 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU HIS A 384 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU HIS A 385 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU HIS A 386 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU HIS A 387 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU HIS A 388 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU HIS A 389 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU ALA B 304 UNP Q9BY41 GLY 304 ENGINEERED MUTATION SEQADV 5THU ILE B 378 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU GLU B 379 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU GLY B 380 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU ARG B 381 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU GLY B 382 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU SER B 383 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU HIS B 384 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU HIS B 385 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU HIS B 386 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU HIS B 387 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU HIS B 388 UNP Q9BY41 EXPRESSION TAG SEQADV 5THU HIS B 389 UNP Q9BY41 EXPRESSION TAG SEQRES 1 A 389 MET GLU GLU PRO GLU GLU PRO ALA ASP SER GLY GLN SER SEQRES 2 A 389 LEU VAL PRO VAL TYR ILE TYR SER PRO GLU TYR VAL SER SEQRES 3 A 389 MET CYS ASP SER LEU ALA LYS ILE PRO LYS ARG ALA SER SEQRES 4 A 389 MET VAL HIS SER LEU ILE GLU ALA TYR ALA LEU HIS LYS SEQRES 5 A 389 GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SER MET GLU SEQRES 6 A 389 GLU MET ALA THR PHE HIS THR ASP ALA TYR LEU GLN HIS SEQRES 7 A 389 LEU GLN LYS VAL SER GLN GLU GLY ASP ASP ASP HIS PRO SEQRES 8 A 389 ASP SER ILE GLU TYR GLY LEU GLY TYR ASP CYS PRO ALA SEQRES 9 A 389 THR GLU GLY ILE PHE ASP TYR ALA ALA ALA ILE GLY GLY SEQRES 10 A 389 ALA THR ILE THR ALA ALA GLN CYS LEU ILE ASP GLY MET SEQRES 11 A 389 CYS LYS VAL ALA ILE ASN TRP SER GLY GLY TRP HIS HIS SEQRES 12 A 389 ALA LYS LYS ASP GLU ALA SER GLY PHE CYS TYR LEU ASN SEQRES 13 A 389 ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG ARG LYS PHE SEQRES 14 A 389 GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU HIS HIS GLY SEQRES 15 A 389 ASP GLY VAL GLU ASP ALA PHE SER PHE THR SER LYS VAL SEQRES 16 A 389 MET THR VAL SER LEU HIS LYS PHE SER PRO GLY PHE PHE SEQRES 17 A 389 PRO GLY THR GLY ASP VAL SER ASP VAL GLY LEU GLY LYS SEQRES 18 A 389 GLY ARG TYR TYR SER VAL ASN VAL PRO ILE GLN ASP GLY SEQRES 19 A 389 ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS GLU SER VAL SEQRES 20 A 389 LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO LYS ALA VAL SEQRES 21 A 389 VAL LEU GLN LEU GLY ALA ASP THR ILE ALA GLY ASP PRO SEQRES 22 A 389 MET CYS SER PHE ASN MET THR PRO VAL GLY ILE GLY LYS SEQRES 23 A 389 CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU ALA THR LEU SEQRES 24 A 389 ILE LEU GLY GLY ALA GLY TYR ASN LEU ALA ASN THR ALA SEQRES 25 A 389 ARG CYS TRP THR TYR LEU THR GLY VAL ILE LEU GLY LYS SEQRES 26 A 389 THR LEU SER SER GLU ILE PRO ASP HIS GLU PHE PHE THR SEQRES 27 A 389 ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE THR PRO SER SEQRES 28 A 389 CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG ILE GLN GLN SEQRES 29 A 389 ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS HIS VAL VAL SEQRES 30 A 389 ILE GLU GLY ARG GLY SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 389 MET GLU GLU PRO GLU GLU PRO ALA ASP SER GLY GLN SER SEQRES 2 B 389 LEU VAL PRO VAL TYR ILE TYR SER PRO GLU TYR VAL SER SEQRES 3 B 389 MET CYS ASP SER LEU ALA LYS ILE PRO LYS ARG ALA SER SEQRES 4 B 389 MET VAL HIS SER LEU ILE GLU ALA TYR ALA LEU HIS LYS SEQRES 5 B 389 GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SER MET GLU SEQRES 6 B 389 GLU MET ALA THR PHE HIS THR ASP ALA TYR LEU GLN HIS SEQRES 7 B 389 LEU GLN LYS VAL SER GLN GLU GLY ASP ASP ASP HIS PRO SEQRES 8 B 389 ASP SER ILE GLU TYR GLY LEU GLY TYR ASP CYS PRO ALA SEQRES 9 B 389 THR GLU GLY ILE PHE ASP TYR ALA ALA ALA ILE GLY GLY SEQRES 10 B 389 ALA THR ILE THR ALA ALA GLN CYS LEU ILE ASP GLY MET SEQRES 11 B 389 CYS LYS VAL ALA ILE ASN TRP SER GLY GLY TRP HIS HIS SEQRES 12 B 389 ALA LYS LYS ASP GLU ALA SER GLY PHE CYS TYR LEU ASN SEQRES 13 B 389 ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG ARG LYS PHE SEQRES 14 B 389 GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU HIS HIS GLY SEQRES 15 B 389 ASP GLY VAL GLU ASP ALA PHE SER PHE THR SER LYS VAL SEQRES 16 B 389 MET THR VAL SER LEU HIS LYS PHE SER PRO GLY PHE PHE SEQRES 17 B 389 PRO GLY THR GLY ASP VAL SER ASP VAL GLY LEU GLY LYS SEQRES 18 B 389 GLY ARG TYR TYR SER VAL ASN VAL PRO ILE GLN ASP GLY SEQRES 19 B 389 ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS GLU SER VAL SEQRES 20 B 389 LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO LYS ALA VAL SEQRES 21 B 389 VAL LEU GLN LEU GLY ALA ASP THR ILE ALA GLY ASP PRO SEQRES 22 B 389 MET CYS SER PHE ASN MET THR PRO VAL GLY ILE GLY LYS SEQRES 23 B 389 CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU ALA THR LEU SEQRES 24 B 389 ILE LEU GLY GLY ALA GLY TYR ASN LEU ALA ASN THR ALA SEQRES 25 B 389 ARG CYS TRP THR TYR LEU THR GLY VAL ILE LEU GLY LYS SEQRES 26 B 389 THR LEU SER SER GLU ILE PRO ASP HIS GLU PHE PHE THR SEQRES 27 B 389 ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE THR PRO SER SEQRES 28 B 389 CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG ILE GLN GLN SEQRES 29 B 389 ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS HIS VAL VAL SEQRES 30 B 389 ILE GLU GLY ARG GLY SER HIS HIS HIS HIS HIS HIS HET ZN A 401 1 HET K A 402 1 HET K A 403 1 HET B3N A 404 22 HET ZN B 401 1 HET K B 402 1 HET K B 403 1 HET B3N B 404 22 HET GGG B 405 13 HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM B3N 4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7- HETNAM 2 B3N OXOHEPTYL]BENZAMIDE HETNAM GGG GLYCYLGLYCYLGLYCINE HETSYN B3N M344 FORMUL 3 ZN 2(ZN 2+) FORMUL 4 K 4(K 1+) FORMUL 6 B3N 2(C16 H25 N3 O3) FORMUL 11 GGG C6 H11 N3 O4 FORMUL 12 HOH *387(H2 O) HELIX 1 AA1 SER A 21 SER A 30 1 10 HELIX 2 AA2 LYS A 36 TYR A 48 1 13 HELIX 3 AA3 ALA A 49 MET A 54 5 6 HELIX 4 AA4 SER A 63 ALA A 68 1 6 HELIX 5 AA5 THR A 72 SER A 83 1 12 HELIX 6 AA6 GLY A 107 ASP A 128 1 22 HELIX 7 AA7 ASN A 156 ARG A 166 1 11 HELIX 8 AA8 GLY A 182 SER A 190 1 9 HELIX 9 AA9 LEU A 219 ARG A 223 5 5 HELIX 10 AB1 GLN A 236 ASN A 256 1 21 HELIX 11 AB2 GLY A 265 ILE A 269 5 5 HELIX 12 AB3 THR A 280 GLN A 293 1 14 HELIX 13 AB4 ASN A 307 LEU A 323 1 17 HELIX 14 AB5 PHE A 336 GLY A 341 5 6 HELIX 15 AB6 GLU A 358 LYS A 374 1 17 HELIX 16 AB7 SER B 21 ASP B 29 1 9 HELIX 17 AB8 LYS B 36 TYR B 48 1 13 HELIX 18 AB9 ALA B 49 MET B 54 5 6 HELIX 19 AC1 SER B 63 ALA B 68 1 6 HELIX 20 AC2 THR B 72 GLU B 85 1 14 HELIX 21 AC3 GLY B 107 ASP B 128 1 22 HELIX 22 AC4 ASN B 156 ARG B 166 1 11 HELIX 23 AC5 GLY B 182 PHE B 189 1 8 HELIX 24 AC6 LEU B 219 ARG B 223 5 5 HELIX 25 AC7 GLN B 236 ASN B 256 1 21 HELIX 26 AC8 GLY B 265 ILE B 269 5 5 HELIX 27 AC9 THR B 280 GLN B 293 1 14 HELIX 28 AD1 ASN B 307 GLY B 324 1 18 HELIX 29 AD2 PHE B 336 GLY B 341 5 6 HELIX 30 AD3 GLU B 358 LYS B 374 1 17 SHEET 1 AA1 8 ARG A 55 VAL A 57 0 SHEET 2 AA1 8 VAL A 17 ILE A 19 1 N TYR A 18 O ARG A 55 SHEET 3 AA1 8 VAL A 133 ASN A 136 1 O VAL A 133 N VAL A 17 SHEET 4 AA1 8 ALA A 297 LEU A 301 1 O ILE A 300 N ALA A 134 SHEET 5 AA1 8 ALA A 259 GLN A 263 1 N LEU A 262 O LEU A 301 SHEET 6 AA1 8 ILE A 172 ASP A 176 1 N VAL A 175 O GLN A 263 SHEET 7 AA1 8 VAL A 195 LYS A 202 1 O MET A 196 N TYR A 174 SHEET 8 AA1 8 SER A 226 ILE A 231 1 O VAL A 227 N THR A 197 SHEET 1 AA2 8 ARG B 55 VAL B 57 0 SHEET 2 AA2 8 VAL B 17 ILE B 19 1 N TYR B 18 O ARG B 55 SHEET 3 AA2 8 VAL B 133 ASN B 136 1 O ILE B 135 N VAL B 17 SHEET 4 AA2 8 ALA B 297 LEU B 301 1 O ILE B 300 N ASN B 136 SHEET 5 AA2 8 ALA B 259 GLN B 263 1 N LEU B 262 O LEU B 301 SHEET 6 AA2 8 ILE B 172 ASP B 176 1 N VAL B 175 O GLN B 263 SHEET 7 AA2 8 VAL B 195 LYS B 202 1 O MET B 196 N TYR B 174 SHEET 8 AA2 8 SER B 226 ILE B 231 1 O VAL B 227 N THR B 197 LINK O ASP A 176 K K A 402 1555 1555 2.78 LINK OD1 ASP A 176 K K A 402 1555 1555 2.75 LINK OD2 ASP A 178 ZN ZN A 401 1555 1555 2.00 LINK O ASP A 178 K K A 402 1555 1555 2.63 LINK ND1 HIS A 180 ZN ZN A 401 1555 1555 2.04 LINK O HIS A 180 K K A 402 1555 1555 2.77 LINK O PHE A 189 K K A 403 1555 1555 2.62 LINK O THR A 192 K K A 403 1555 1555 2.71 LINK O VAL A 195 K K A 403 1555 1555 2.60 LINK OG SER A 199 K K A 402 1555 1555 2.83 LINK O LEU A 200 K K A 402 1555 1555 2.59 LINK O TYR A 225 K K A 403 1555 1555 3.11 LINK OD2 ASP A 267 ZN ZN A 401 1555 1555 1.98 LINK ZN ZN A 401 O4 B3N A 404 1555 1555 2.00 LINK ZN ZN A 401 O2 B3N A 404 1555 1555 2.44 LINK K K A 403 O HOH A 529 1555 1555 2.80 LINK K K A 403 O HOH A 630 1555 1555 2.80 LINK O ASP B 176 K K B 402 1555 1555 2.77 LINK OD1 ASP B 176 K K B 402 1555 1555 2.72 LINK OD2 ASP B 178 ZN ZN B 401 1555 1555 2.01 LINK O ASP B 178 K K B 402 1555 1555 2.60 LINK ND1 HIS B 180 ZN ZN B 401 1555 1555 2.03 LINK O HIS B 180 K K B 402 1555 1555 2.73 LINK O PHE B 189 K K B 403 1555 1555 2.60 LINK O THR B 192 K K B 403 1555 1555 2.84 LINK O VAL B 195 K K B 403 1555 1555 2.58 LINK OG SER B 199 K K B 402 1555 1555 2.83 LINK O LEU B 200 K K B 402 1555 1555 2.58 LINK O TYR B 225 K K B 403 1555 1555 3.14 LINK OD2 ASP B 267 ZN ZN B 401 1555 1555 1.95 LINK ZN ZN B 401 O2 B3N B 404 1555 1555 2.34 LINK ZN ZN B 401 O4 B3N B 404 1555 1555 2.25 LINK K K B 403 O HOH B 526 1555 1555 2.69 LINK K K B 403 O HOH B 611 1555 1555 2.74 CISPEP 1 PHE A 208 PRO A 209 0 -3.68 CISPEP 2 GLY A 341 PRO A 342 0 2.16 CISPEP 3 PHE B 208 PRO B 209 0 -3.98 CISPEP 4 GLY B 341 PRO B 342 0 5.64 SITE 1 AC1 5 ASP A 178 HIS A 180 ASP A 267 ALA A 304 SITE 2 AC1 5 B3N A 404 SITE 1 AC2 5 ASP A 176 ASP A 178 HIS A 180 SER A 199 SITE 2 AC2 5 LEU A 200 SITE 1 AC3 6 PHE A 189 THR A 192 VAL A 195 TYR A 225 SITE 2 AC3 6 HOH A 529 HOH A 630 SITE 1 AC4 16 HIS A 142 HIS A 143 GLY A 151 ASP A 178 SITE 2 AC4 16 HIS A 180 PHE A 208 ASP A 267 ALA A 304 SITE 3 AC4 16 TYR A 306 ZN A 401 HOH A 622 PHE B 152 SITE 4 AC4 16 PRO B 273 MET B 274 TYR B 306 B3N B 404 SITE 1 AC5 5 ASP B 178 HIS B 180 ASP B 267 ALA B 304 SITE 2 AC5 5 B3N B 404 SITE 1 AC6 5 ASP B 176 ASP B 178 HIS B 180 SER B 199 SITE 2 AC6 5 LEU B 200 SITE 1 AC7 6 PHE B 189 THR B 192 VAL B 195 TYR B 225 SITE 2 AC7 6 HOH B 526 HOH B 611 SITE 1 AC8 16 PHE A 152 PRO A 273 MET A 274 TYR A 306 SITE 2 AC8 16 B3N A 404 HIS B 142 HIS B 143 PHE B 152 SITE 3 AC8 16 ASP B 178 HIS B 180 PHE B 208 ASP B 267 SITE 4 AC8 16 ALA B 304 TYR B 306 ZN B 401 HOH B 590 SITE 1 AC9 3 GLU B 335 PHE B 336 THR B 338 CRYST1 53.500 83.950 98.400 90.00 101.83 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018692 0.000000 0.003915 0.00000 SCALE2 0.000000 0.011912 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010383 0.00000