HEADER HYDROLASE/HYDROLASE INHIBITOR 29-JAN-20 6VNQ TITLE CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 10 IN COMPLEX TITLE 2 WITH BISHYDROXAMIC ACID BASED INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYAMINE DEACETYLASE HDAC10; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HISTONE DEACETYLASE 10; COMPND 5 EC: 3.5.1.48,3.5.1.62; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: HDAC10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE DEACETYLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.J.HERBST-GERVASONI,D.W.CHRISTIANSON REVDAT 3 11-OCT-23 6VNQ 1 LINK REVDAT 2 15-JUL-20 6VNQ 1 JRNL REVDAT 1 13-MAY-20 6VNQ 0 JRNL AUTH M.MORGEN,R.R.STEIMBACH,M.GERALDY,L.HELLWEG,P.SEHR, JRNL AUTH 2 J.RIDINGER,O.WITT,I.OEHME,C.J.HERBST-GERVASONI,J.D.OSKO, JRNL AUTH 3 N.J.PORTER,D.W.CHRISTIANSON,N.GUNKEL,A.K.MILLER JRNL TITL DESIGN AND SYNTHESIS OF DIHYDROXAMIC ACIDS AS HDAC6/8/10 JRNL TITL 2 INHIBITORS. JRNL REF CHEMMEDCHEM V. 15 1163 2020 JRNL REFN ESSN 1860-7187 JRNL PMID 32348628 JRNL DOI 10.1002/CMDC.202000149 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 58982 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190 REMARK 3 FREE R VALUE TEST SET COUNT : 3062 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 69.7600 - 5.7400 1.00 2746 169 0.1751 0.2263 REMARK 3 2 5.7400 - 4.5600 1.00 2635 151 0.1535 0.1746 REMARK 3 3 4.5600 - 3.9800 1.00 2602 135 0.1435 0.1640 REMARK 3 4 3.9800 - 3.6200 1.00 2550 153 0.1620 0.1914 REMARK 3 5 3.6200 - 3.3600 1.00 2563 136 0.1884 0.2105 REMARK 3 6 3.3600 - 3.1600 1.00 2563 145 0.1947 0.2460 REMARK 3 7 3.1600 - 3.0000 1.00 2553 115 0.2047 0.2268 REMARK 3 8 3.0000 - 2.8700 1.00 2522 152 0.2051 0.2479 REMARK 3 9 2.8700 - 2.7600 1.00 2554 140 0.2097 0.2604 REMARK 3 10 2.7600 - 2.6700 1.00 2506 151 0.2128 0.2716 REMARK 3 11 2.6700 - 2.5800 1.00 2518 123 0.2109 0.2700 REMARK 3 12 2.5800 - 2.5100 1.00 2524 145 0.2196 0.2744 REMARK 3 13 2.5100 - 2.4400 1.00 2505 133 0.2136 0.2878 REMARK 3 14 2.4400 - 2.3800 1.00 2584 105 0.2310 0.2709 REMARK 3 15 2.3800 - 2.3300 1.00 2491 148 0.2333 0.2927 REMARK 3 16 2.3300 - 2.2800 1.00 2522 147 0.2409 0.2830 REMARK 3 17 2.2800 - 2.2300 1.00 2484 140 0.2564 0.3311 REMARK 3 18 2.2300 - 2.1900 1.00 2517 131 0.2548 0.3048 REMARK 3 19 2.1900 - 2.1500 1.00 2508 130 0.2569 0.2647 REMARK 3 20 2.1500 - 2.1200 1.00 2497 119 0.2709 0.3297 REMARK 3 21 2.1200 - 2.0800 1.00 2502 156 0.2862 0.3086 REMARK 3 22 2.0800 - 2.0500 1.00 2474 138 0.3180 0.3603 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) : 0.273 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.03 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 : 0.009 5064 REMARK 3 ANGLE : 0.983 6915 REMARK 3 CHIRALITY : 0.192 789 REMARK 3 PLANARITY : 0.007 891 REMARK 3 DIHEDRAL : 22.534 1801 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 6VNQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000246702. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-19 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58990 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 69.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.34900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 5TD7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML HDAC10, 2 MM INHIBITOR, REMARK 280 1:1000 TRYPSIN:HDAC10, 0.168 M POTASSIUM PHOSPHATE MONOBASIC, REMARK 280 0.032 M POTASSIUM PHOSPHATE DIBASIC, AND 20% PEG3350 (V/V), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 81.79000 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 163.58000 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 163.58000 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 81.79000 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 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 400 REMARK 400 COMPOUND REMARK 400 THE SEQUENCE CONFLICTS ARE DUE TO UNIPROT UPDATING THE REFERENCE REMARK 400 SEQUENCE ARE THE AUTHORS HAD CLONED THEIR SEQUENCE. 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 THR A 367 REMARK 465 ASN A 368 REMARK 465 PRO A 369 REMARK 465 LYS A 370 REMARK 465 ARG A 371 REMARK 465 PRO A 372 REMARK 465 ARG A 373 REMARK 465 LEU A 374 REMARK 465 ASP A 375 REMARK 465 ALA A 376 REMARK 465 THR A 377 REMARK 465 ASN A 378 REMARK 465 GLY A 379 REMARK 465 GLY A 380 REMARK 465 PRO A 381 REMARK 465 LYS A 382 REMARK 465 GLU A 383 REMARK 465 SER A 384 REMARK 465 SER A 385 REMARK 465 GLU A 386 REMARK 465 PRO A 387 REMARK 465 ALA A 388 REMARK 465 SER A 389 REMARK 465 GLU A 390 REMARK 465 SER A 391 REMARK 465 ASN A 392 REMARK 465 PRO A 393 REMARK 465 LYS A 394 REMARK 465 LYS A 395 REMARK 465 THR A 396 REMARK 465 ALA A 397 REMARK 465 GLN A 398 REMARK 465 GLY A 435 REMARK 465 ASP A 436 REMARK 465 ALA A 589 REMARK 465 ALA A 590 REMARK 465 LYS A 591 REMARK 465 THR A 592 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 ARG A 41 CZ NH1 NH2 REMARK 470 GLN A 60 CG CD OE1 NE2 REMARK 470 GLU A 72 CD OE1 OE2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 SER A 365 OG REMARK 470 ASP A 399 CG OD1 OD2 REMARK 470 LYS A 407 CG CD CE NZ REMARK 470 MET A 409 CG SD CE REMARK 470 GLU A 424 CG CD OE1 OE2 REMARK 470 THR A 426 OG1 CG2 REMARK 470 LYS A 429 CG CD CE NZ REMARK 470 GLU A 439 CG CD OE1 OE2 REMARK 470 LYS A 443 CG CD CE NZ REMARK 470 GLN A 446 OE1 NE2 REMARK 470 HIS A 454 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 455 CG OD1 OD2 REMARK 470 GLN A 459 CG CD OE1 NE2 REMARK 470 ASN A 460 CG OD1 ND2 REMARK 470 ARG A 463 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 477 CG CD NE CZ NH1 NH2 REMARK 470 SER A 478 OG REMARK 470 ASP A 479 CG OD1 OD2 REMARK 470 GLU A 480 CG CD OE1 OE2 REMARK 470 GLU A 519 CG CD OE1 OE2 REMARK 470 LYS A 523 CE NZ REMARK 470 LYS A 537 CG CD CE NZ REMARK 470 GLU A 538 CG CD OE1 OE2 REMARK 470 GLU A 540 CG CD OE1 OE2 REMARK 470 LYS A 542 CG CD CE NZ REMARK 470 ARG A 546 CD NE CZ NH1 NH2 REMARK 470 ARG A 552 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 553 CG CD OE1 OE2 REMARK 470 GLU A 555 CG CD OE1 OE2 REMARK 470 LEU A 557 CG CD1 CD2 REMARK 470 GLN A 563 OE1 NE2 REMARK 470 THR A 588 OG1 CG2 REMARK 470 ARG A 593 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 594 CG CD1 CD2 REMARK 470 ARG A 596 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 622 CG CD CE NZ REMARK 470 LEU A 643 CG CD1 CD2 REMARK 470 ARG A 644 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 647 CD CE NZ REMARK 470 LYS A 656 CD CE NZ REMARK 470 GLU A 674 CG CD OE1 OE2 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 ARG A 15 44.34 -104.48 REMARK 500 ASP A 22 97.35 -169.50 REMARK 500 PHE A 146 -2.70 69.59 REMARK 500 TYR A 199 -50.84 -133.00 REMARK 500 VAL A 247 -68.56 -127.87 REMARK 500 ASP A 256 64.99 60.07 REMARK 500 ASP A 267 0.46 -67.23 REMARK 500 GLU A 304 -106.98 -110.10 REMARK 500 SER A 357 -74.51 -48.38 REMARK 500 SER A 358 -7.40 -53.10 REMARK 500 LEU A 362 -157.63 -117.17 REMARK 500 ALA A 363 -78.66 -101.23 REMARK 500 THR A 457 -8.03 -140.74 REMARK 500 ASP A 458 107.15 -53.13 REMARK 500 ASP A 479 11.09 55.52 REMARK 500 LEU A 568 -57.50 -122.75 REMARK 500 MET A 595 61.65 -113.89 REMARK 500 ARG A 596 18.28 -68.08 REMARK 500 ARG A 610 29.17 49.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLN A 139 -12.64 REMARK 500 GLN A 139 -12.21 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 A 705 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 172 O REMARK 620 2 ASP A 172 OD2 70.5 REMARK 620 3 ASP A 174 O 94.8 100.0 REMARK 620 4 HIS A 176 O 169.3 98.8 86.2 REMARK 620 5 SER A 195 OG 88.0 113.8 144.9 97.3 REMARK 620 6 TRP A 196 O 87.2 155.6 71.2 103.2 74.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 704 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 174 OD2 REMARK 620 2 HIS A 176 ND1 105.5 REMARK 620 3 ASP A 267 OD2 104.7 92.0 REMARK 620 4 R5G A 701 N02 115.0 84.1 139.8 REMARK 620 5 R5G A 701 N02 166.6 83.4 84.6 55.2 REMARK 620 6 R5G A 701 O01 93.8 113.0 143.8 31.6 73.3 REMARK 620 7 R5G A 701 O01 136.4 117.1 83.5 63.5 33.7 62.2 REMARK 620 8 HOH A 801 O 83.0 103.3 160.5 33.8 85.3 17.0 78.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 706 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 185 O REMARK 620 2 ASP A 188 O 74.3 REMARK 620 3 VAL A 191 O 123.9 75.2 REMARK 620 4 PHE A 224 O 154.3 119.3 81.7 REMARK 620 5 HOH A 860 O 76.7 90.7 148.7 81.3 REMARK 620 6 HOH A 977 O 70.3 144.4 122.7 94.9 84.9 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 R5G A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 708 DBREF 6VNQ A 2 675 UNP F1QCV2 HDA10_DANRE 2 675 SEQADV 6VNQ ALA A 1 UNP F1QCV2 EXPRESSION TAG SEQADV 6VNQ GLU A 24 UNP F1QCV2 ALA 24 ENGINEERED MUTATION SEQADV 6VNQ ALA A 94 UNP F1QCV2 ASP 94 ENGINEERED MUTATION SEQADV 6VNQ PHE A 154 UNP F1QCV2 ILE 154 CONFLICT SEQADV 6VNQ THR A 548 UNP F1QCV2 SER 548 CONFLICT SEQADV 6VNQ GLU A 586 UNP F1QCV2 GLY 586 CONFLICT SEQADV 6VNQ ARG A 593 UNP F1QCV2 GLY 593 CONFLICT SEQADV 6VNQ ARG A 596 UNP F1QCV2 THR 596 CONFLICT SEQADV 6VNQ MET A 613 UNP F1QCV2 THR 613 CONFLICT SEQADV 6VNQ PRO A 646 UNP F1QCV2 LEU 646 CONFLICT SEQADV 6VNQ TRP A 676 UNP F1QCV2 EXPRESSION TAG SEQRES 1 A 676 ALA ALA SER GLY SER ALA LEU ILE PHE ASP GLU GLU MET SEQRES 2 A 676 SER ARG TYR LYS LEU LEU TRP THR ASP PRO GLU CYS GLU SEQRES 3 A 676 ILE GLU VAL PRO GLU ARG LEU THR VAL SER TYR GLU ALA SEQRES 4 A 676 LEU ARG THR HIS GLY LEU ALA GLN ARG CYS LYS ALA VAL SEQRES 5 A 676 PRO VAL ARG GLN ALA THR GLU GLN GLU ILE LEU LEU ALA SEQRES 6 A 676 HIS SER GLU GLU TYR LEU GLU ALA VAL LYS GLN THR PRO SEQRES 7 A 676 GLY MET ASN VAL GLU GLU LEU MET ALA PHE SER LYS LYS SEQRES 8 A 676 TYR ASN ALA VAL TYR PHE HIS GLN ASN ILE TYR HIS CYS SEQRES 9 A 676 ALA LYS LEU ALA ALA GLY ALA THR LEU GLN LEU VAL ASP SEQRES 10 A 676 SER VAL MET LYS ARG GLU VAL ARG ASN GLY MET ALA LEU SEQRES 11 A 676 VAL ARG PRO PRO GLY HIS HIS SER GLN ARG SER ALA ALA SEQRES 12 A 676 ASN GLY PHE CYS VAL PHE ASN ASN VAL ALA PHE ALA ALA SEQRES 13 A 676 LEU TYR ALA LYS LYS ASN TYR ASN LEU ASN ARG ILE LEU SEQRES 14 A 676 ILE VAL ASP TRP ASP VAL HIS HIS GLY GLN GLY ILE GLN SEQRES 15 A 676 TYR CYS PHE GLU GLU ASP PRO SER VAL LEU TYR PHE SER SEQRES 16 A 676 TRP HIS ARG TYR GLU HIS GLN SER PHE TRP PRO ASN LEU SEQRES 17 A 676 PRO GLU SER ASP TYR SER SER VAL GLY LYS GLY LYS GLY SEQRES 18 A 676 SER GLY PHE ASN ILE ASN LEU PRO TRP ASN LYS VAL GLY SEQRES 19 A 676 MET THR ASN SER ASP TYR LEU ALA ALA PHE PHE HIS VAL SEQRES 20 A 676 LEU LEU PRO VAL ALA TYR GLU PHE ASP PRO GLU LEU VAL SEQRES 21 A 676 ILE VAL SER ALA GLY PHE ASP SER ALA ILE GLY ASP PRO SEQRES 22 A 676 GLU GLY GLU MET CYS ALA LEU PRO GLU ILE PHE ALA HIS SEQRES 23 A 676 LEU THR HIS LEU LEU MET PRO LEU ALA ALA GLY LYS MET SEQRES 24 A 676 CYS VAL VAL LEU GLU GLY GLY TYR ASN LEU THR SER LEU SEQRES 25 A 676 GLY GLN SER VAL CYS GLN THR VAL HIS SER LEU LEU GLY SEQRES 26 A 676 ASP PRO THR PRO ARG ILE SER GLY LEU GLY THR ALA CYS SEQRES 27 A 676 ASP SER ALA LEU GLU SER ILE GLN ASN VAL ARG ASN VAL SEQRES 28 A 676 GLN SER SER TYR TRP SER SER PHE LYS HIS LEU ALA GLN SEQRES 29 A 676 SER GLU THR ASN PRO LYS ARG PRO ARG LEU ASP ALA THR SEQRES 30 A 676 ASN GLY GLY PRO LYS GLU SER SER GLU PRO ALA SER GLU SEQRES 31 A 676 SER ASN PRO LYS LYS THR ALA GLN ASP ILE VAL TRP PRO SEQRES 32 A 676 GLU PRO LEU LYS ARG MET PRO ALA SER VAL ARG THR VAL SEQRES 33 A 676 VAL VAL PRO PRO PRO GLY VAL GLU LEU THR LEU PRO LYS SEQRES 34 A 676 ASN CYS GLN HIS SER GLY ASP ILE SER GLU SER THR ALA SEQRES 35 A 676 LYS GLU VAL GLN ARG ILE ARG ASP LYS HIS PHE HIS ASP SEQRES 36 A 676 LEU THR ASP GLN ASN ILE LEU ARG SER LEU GLY ASN ILE SEQRES 37 A 676 ILE SER VAL LEU ASP ARG MET MET ARG SER ASP GLU VAL SEQRES 38 A 676 CYS ASN GLY CYS VAL VAL VAL SER ASP LEU SER VAL SER SEQRES 39 A 676 VAL GLN CYS ALA LEU GLN HIS ALA LEU THR GLU PRO ALA SEQRES 40 A 676 GLU ARG VAL LEU VAL VAL TYR VAL GLY ASP GLY GLU LEU SEQRES 41 A 676 PRO VAL LYS THR ASN ASP GLY LYS VAL PHE LEU VAL GLN SEQRES 42 A 676 ILE CYS THR LYS GLU THR GLU ASP LYS CYS VAL ASN ARG SEQRES 43 A 676 LEU THR LEU CYS LEU ARG GLU GLY GLU SER LEU THR ALA SEQRES 44 A 676 GLY PHE MET GLN ALA LEU LEU GLY LEU ILE LEU PRO VAL SEQRES 45 A 676 ALA TYR GLU PHE ASN PRO ALA LEU VAL LEU GLY ILE VAL SEQRES 46 A 676 GLU GLU THR ALA ALA LYS THR ARG LEU MET ARG VAL TRP SEQRES 47 A 676 GLY HIS MET THR CYS LEU ILE GLN GLY LEU ALA ARG GLY SEQRES 48 A 676 ARG MET LEU THR LEU LEU GLN GLY TYR ASP LYS ASP LEU SEQRES 49 A 676 LEU GLU LEU THR VAL SER ALA LEU SER GLY ALA SER ILE SEQRES 50 A 676 SER PRO LEU GLY PRO LEU ARG ALA PRO LYS PRO GLU ASP SEQRES 51 A 676 VAL GLU MET MET GLU LYS GLN ARG GLN ARG LEU GLN GLU SEQRES 52 A 676 ARG TRP GLY LEU LEU ARG CYS THR VAL SER GLU SER TRP HET R5G A 701 48 HET EDO A 702 4 HET EDO A 703 4 HET ZN A 704 1 HET K A 705 1 HET K A 706 1 HET PO4 A 707 5 HET PO4 A 708 5 HETNAM R5G N-HYDROXY-1-{[4-(HYDROXYCARBAMOYL)PHENYL]METHYL}-1H- HETNAM 2 R5G INDOLE-6-CARBOXAMIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM PO4 PHOSPHATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 R5G C17 H15 N3 O4 FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 ZN ZN 2+ FORMUL 6 K 2(K 1+) FORMUL 8 PO4 2(O4 P 3-) FORMUL 10 HOH *261(H2 O) HELIX 1 AA1 ASP A 10 ARG A 15 5 6 HELIX 2 AA2 PRO A 30 HIS A 43 1 14 HELIX 3 AA3 LEU A 45 CYS A 49 5 5 HELIX 4 AA4 THR A 58 LEU A 63 1 6 HELIX 5 AA5 SER A 67 GLN A 76 1 10 HELIX 6 AA6 THR A 77 MET A 80 5 4 HELIX 7 AA7 ASN A 81 LYS A 90 1 10 HELIX 8 AA8 ASN A 100 LYS A 121 1 22 HELIX 9 AA9 ASN A 150 ASN A 164 1 15 HELIX 10 AB1 GLY A 178 GLU A 186 1 9 HELIX 11 AB2 LEU A 208 ASP A 212 5 5 HELIX 12 AB3 LYS A 218 SER A 222 5 5 HELIX 13 AB4 THR A 236 VAL A 247 1 12 HELIX 14 AB5 VAL A 247 ASP A 256 1 10 HELIX 15 AB6 PRO A 281 MET A 292 1 12 HELIX 16 AB7 PRO A 293 GLY A 297 5 5 HELIX 17 AB8 ASN A 308 LEU A 324 1 17 HELIX 18 AB9 CYS A 338 SER A 353 1 16 HELIX 19 AC1 SER A 354 TYR A 355 5 2 HELIX 20 AC2 TRP A 356 LYS A 360 5 5 HELIX 21 AC3 SER A 438 PHE A 453 1 16 HELIX 22 AC4 ASN A 460 ARG A 477 1 18 HELIX 23 AC5 ASP A 490 THR A 504 1 15 HELIX 24 AC6 SER A 556 LEU A 568 1 13 HELIX 25 AC7 LEU A 568 ASN A 577 1 10 HELIX 26 AC8 VAL A 597 GLN A 606 1 10 HELIX 27 AC9 GLY A 607 GLY A 611 5 5 HELIX 28 AD1 ASP A 621 SER A 633 1 13 HELIX 29 AD2 LYS A 647 GLN A 662 1 16 HELIX 30 AD3 TRP A 665 ARG A 669 5 5 SHEET 1 AA1 7 SER A 5 ILE A 8 0 SHEET 2 AA1 7 ASN A 126 ALA A 129 1 O MET A 128 N ILE A 8 SHEET 3 AA1 7 MET A 299 LEU A 303 1 O VAL A 301 N GLY A 127 SHEET 4 AA1 7 LEU A 259 ALA A 264 1 N VAL A 262 O CYS A 300 SHEET 5 AA1 7 ILE A 168 ASP A 172 1 N LEU A 169 O ILE A 261 SHEET 6 AA1 7 VAL A 191 ARG A 198 1 O LEU A 192 N ILE A 170 SHEET 7 AA1 7 ASN A 225 TRP A 230 1 O TRP A 230 N HIS A 197 SHEET 1 AA2 8 CYS A 431 HIS A 433 0 SHEET 2 AA2 8 VAL A 413 VAL A 418 1 N VAL A 417 O GLN A 432 SHEET 3 AA2 8 VAL A 481 VAL A 488 1 O ASN A 483 N ARG A 414 SHEET 4 AA2 8 MET A 613 GLN A 618 1 O LEU A 617 N VAL A 488 SHEET 5 AA2 8 LEU A 580 VAL A 585 1 N GLY A 583 O LEU A 616 SHEET 6 AA2 8 VAL A 510 VAL A 515 1 N LEU A 511 O LEU A 582 SHEET 7 AA2 8 VAL A 529 CYS A 535 1 O VAL A 532 N VAL A 512 SHEET 8 AA2 8 ARG A 546 CYS A 550 1 O LEU A 549 N GLN A 533 LINK O ASP A 172 K K A 705 1555 1555 2.94 LINK OD2 ASP A 172 K K A 705 1555 1555 2.71 LINK OD2 ASP A 174 ZN ZN A 704 1555 1555 2.00 LINK O ASP A 174 K K A 705 1555 1555 2.67 LINK ND1 HIS A 176 ZN ZN A 704 1555 1555 2.26 LINK O HIS A 176 K K A 705 1555 1555 2.64 LINK O PHE A 185 K K A 706 1555 1555 2.66 LINK O ASP A 188 K K A 706 1555 1555 2.96 LINK O VAL A 191 K K A 706 1555 1555 2.63 LINK OG SER A 195 K K A 705 1555 1555 2.82 LINK O TRP A 196 K K A 705 1555 1555 2.64 LINK O PHE A 224 K K A 706 1555 1555 2.86 LINK OD2 ASP A 267 ZN ZN A 704 1555 1555 2.08 LINK N02AR5G A 701 ZN ZN A 704 1555 1555 2.56 LINK N02BR5G A 701 ZN ZN A 704 1555 1555 2.36 LINK O01AR5G A 701 ZN ZN A 704 1555 1555 2.36 LINK O01BR5G A 701 ZN ZN A 704 1555 1555 2.11 LINK ZN ZN A 704 O HOH A 801 1555 1555 2.22 LINK K K A 706 O HOH A 860 1555 1555 2.74 LINK K K A 706 O HOH A 977 1555 1555 2.78 CISPEP 1 ARG A 132 PRO A 133 0 0.95 CISPEP 2 TRP A 205 PRO A 206 0 5.90 CISPEP 3 GLU A 505 PRO A 506 0 -1.78 SITE 1 AC1 17 GLU A 24 ASN A 93 ALA A 94 HIS A 136 SITE 2 AC1 17 HIS A 137 GLY A 145 PHE A 146 ASP A 174 SITE 3 AC1 17 HIS A 176 TRP A 205 ASP A 267 GLU A 274 SITE 4 AC1 17 GLY A 305 TYR A 307 ZN A 704 HOH A 801 SITE 5 AC1 17 HOH A 996 SITE 1 AC2 7 LYS A 75 HIS A 201 PO4 A 708 HOH A 809 SITE 2 AC2 7 HOH A 945 HOH A 982 HOH A 983 SITE 1 AC3 4 VAL A 35 GLU A 38 ALA A 39 HOH A 985 SITE 1 AC4 5 ASP A 174 HIS A 176 ASP A 267 R5G A 701 SITE 2 AC4 5 HOH A 801 SITE 1 AC5 5 ASP A 172 ASP A 174 HIS A 176 SER A 195 SITE 2 AC5 5 TRP A 196 SITE 1 AC6 6 PHE A 185 ASP A 188 VAL A 191 PHE A 224 SITE 2 AC6 6 HOH A 860 HOH A 977 SITE 1 AC7 10 GLN A 56 LYS A 106 HIS A 201 ASP A 212 SITE 2 AC7 10 TYR A 213 ASN A 231 HOH A 818 HOH A 827 SITE 3 AC7 10 HOH A 838 HOH A 950 SITE 1 AC8 10 LYS A 75 HIS A 201 ASN A 231 LYS A 232 SITE 2 AC8 10 SER A 340 GLU A 343 EDO A 702 HOH A 816 SITE 3 AC8 10 HOH A 917 HOH A 953 CRYST1 80.549 80.549 245.370 90.00 90.00 120.00 P 31 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 0.012415 0.007168 0.000000 0.00000 SCALE2 0.000000 0.014335 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004075 0.00000