HEADER HYDROLASE 27-MAR-20 6WBQ TITLE CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 10 IN COMPLEX TITLE 2 WITH TUBASTATIN A 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 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 EXPDTA X-RAY DIFFRACTION AUTHOR C.J.HERBST-GERVASONI,D.W.CHRISTIANSON REVDAT 4 18-OCT-23 6WBQ 1 REMARK REVDAT 3 02-SEP-20 6WBQ 1 JRNL REVDAT 2 29-JUL-20 6WBQ 1 JRNL LINK REVDAT 1 22-JUL-20 6WBQ 0 JRNL AUTH C.J.HERBST-GERVASONI,R.R.STEIMBACH,M.MORGEN,A.K.MILLER, JRNL AUTH 2 D.W.CHRISTIANSON JRNL TITL STRUCTURAL BASIS FOR THE SELECTIVE INHIBITION OF HDAC10, THE JRNL TITL 2 CYTOSOLIC POLYAMINE DEACETYLASE. JRNL REF ACS CHEM.BIOL. V. 15 2154 2020 JRNL REFN ESSN 1554-8937 JRNL PMID 32659072 JRNL DOI 10.1021/ACSCHEMBIO.0C00362 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 63789 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 3185 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 53.2400 - 5.6900 1.00 2899 132 0.1758 0.2263 REMARK 3 2 5.6900 - 4.5100 0.99 2718 141 0.1591 0.1924 REMARK 3 3 4.5100 - 3.9400 1.00 2706 137 0.1586 0.1968 REMARK 3 4 3.9400 - 3.5800 1.00 2665 137 0.1761 0.2021 REMARK 3 5 3.5800 - 3.3300 0.99 2648 114 0.1919 0.2215 REMARK 3 6 3.3300 - 3.1300 1.00 2650 153 0.2118 0.2279 REMARK 3 7 3.1300 - 2.9700 1.00 2645 146 0.2110 0.2255 REMARK 3 8 2.9700 - 2.8400 1.00 2627 132 0.2146 0.2838 REMARK 3 9 2.8400 - 2.7300 0.99 2606 164 0.2181 0.2604 REMARK 3 10 2.7300 - 2.6400 0.99 2615 132 0.2170 0.2602 REMARK 3 11 2.6400 - 2.5600 1.00 2638 134 0.2242 0.2346 REMARK 3 12 2.5600 - 2.4800 1.00 2611 137 0.2240 0.2557 REMARK 3 13 2.4800 - 2.4200 1.00 2605 140 0.2261 0.2653 REMARK 3 14 2.4200 - 2.3600 1.00 2597 132 0.2206 0.2777 REMARK 3 15 2.3600 - 2.3100 1.00 2617 140 0.2199 0.2672 REMARK 3 16 2.3100 - 2.2600 0.99 2593 148 0.2311 0.2584 REMARK 3 17 2.2600 - 2.2100 0.99 2589 151 0.2409 0.2756 REMARK 3 18 2.2100 - 2.1700 1.00 2540 158 0.2506 0.2573 REMARK 3 19 2.1700 - 2.1300 1.00 2596 146 0.2565 0.3157 REMARK 3 20 2.1300 - 2.1000 1.00 2664 100 0.2736 0.3210 REMARK 3 21 2.1000 - 2.0600 1.00 2555 148 0.2811 0.3201 REMARK 3 22 2.0600 - 2.0300 1.00 2621 133 0.2942 0.2856 REMARK 3 23 2.0300 - 2.0000 1.00 2599 130 0.3055 0.3258 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) : 0.245 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.483 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.14 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 : 0.007 5020 REMARK 3 ANGLE : 0.887 6840 REMARK 3 CHIRALITY : 0.051 780 REMARK 3 PLANARITY : 0.006 879 REMARK 3 DIHEDRAL : 8.955 4055 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 6WBQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247968. 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 PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63801 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 53.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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 (%): 60.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML HDAC10, 2 MM INHIBITOR, REMARK 280 1:1000 TRYPSIN:HDAC10, 0.158 M SODIUM PHOSPHATE MONOBASIC, 0.023 REMARK 280 M SODIUM PHOSPHATE DIBASIC, 18% PEG3350 (W/V), AND 0.01 M REMARK 280 TAURINE, 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 82.27033 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 164.54067 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 164.54067 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 82.27033 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 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 SER A 365 REMARK 465 GLU A 366 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 HIS A 454 REMARK 465 ASP A 455 REMARK 465 ALA A 589 REMARK 465 ALA A 590 REMARK 465 LYS A 591 REMARK 465 THR A 592 REMARK 465 ARG A 593 REMARK 465 LEU A 643 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 GLU A 11 CD OE1 OE2 REMARK 470 ARG A 41 CD NE CZ NH1 NH2 REMARK 470 GLN A 60 CD OE1 NE2 REMARK 470 GLU A 72 CD OE1 OE2 REMARK 470 LYS A 220 CE NZ REMARK 470 LYS A 360 CE NZ REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 ASP A 399 CG OD1 OD2 REMARK 470 LYS A 407 CG CD CE NZ 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 CD OE1 NE2 REMARK 470 ARG A 449 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 459 CG CD OE1 NE2 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 LYS A 523 CG CD CE NZ REMARK 470 ASN A 525 CG OD1 ND2 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 GLU A 555 CG CD OE1 OE2 REMARK 470 THR A 588 OG1 CG2 REMARK 470 LEU A 594 CG CD1 CD2 REMARK 470 LYS A 622 CG CD CE NZ REMARK 470 ARG A 644 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 48.25 -103.20 REMARK 500 ASP A 22 97.50 -170.06 REMARK 500 PHE A 146 -4.49 67.79 REMARK 500 TYR A 199 -48.84 -130.82 REMARK 500 VAL A 247 -64.74 -130.54 REMARK 500 GLU A 304 -105.78 -106.55 REMARK 500 SER A 358 -19.43 -37.50 REMARK 500 SER A 434 79.14 -168.81 REMARK 500 THR A 457 -23.83 -148.65 REMARK 500 ASP A 458 97.19 -41.87 REMARK 500 LYS A 542 -81.79 -91.60 REMARK 500 LEU A 568 -56.96 -126.33 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 707 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 172 O REMARK 620 2 ASP A 172 OD2 72.0 REMARK 620 3 ASP A 174 O 91.6 97.3 REMARK 620 4 HIS A 176 O 168.5 96.7 87.7 REMARK 620 5 SER A 195 OG 90.1 114.4 147.0 96.7 REMARK 620 6 TRP A 196 O 88.9 158.5 72.9 101.9 74.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 712 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 174 OD2 REMARK 620 2 HIS A 176 ND1 103.7 REMARK 620 3 ASP A 267 OD2 106.5 93.3 REMARK 620 4 N9W A 701 O2 158.5 94.2 84.0 REMARK 620 5 N9W A 701 N1 112.4 82.8 140.7 57.6 REMARK 620 6 N9W A 701 O1 85.6 106.3 154.0 77.8 32.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 708 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 185 O REMARK 620 2 ASP A 188 O 80.9 REMARK 620 3 VAL A 191 O 133.4 78.4 REMARK 620 4 PHE A 224 O 145.3 126.9 77.8 REMARK 620 5 HOH A 862 O 67.6 148.5 124.4 82.4 REMARK 620 6 HOH A 887 O 79.2 94.5 143.4 78.3 79.0 REMARK 620 7 HOH A 971 O 91.6 155.0 90.1 70.7 34.3 107.5 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue N9W 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 EDO A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 708 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 709 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 710 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 711 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 712 DBREF 6WBQ A 2 675 UNP F1QCV2 HDA10_DANRE 2 675 SEQADV 6WBQ ALA A 1 UNP F1QCV2 EXPRESSION TAG SEQADV 6WBQ GLU A 24 UNP F1QCV2 ALA 24 CONFLICT SEQADV 6WBQ ALA A 94 UNP F1QCV2 ASP 94 CONFLICT SEQADV 6WBQ PHE A 154 UNP F1QCV2 ILE 154 CONFLICT SEQADV 6WBQ THR A 548 UNP F1QCV2 SER 548 CONFLICT SEQADV 6WBQ GLU A 586 UNP F1QCV2 GLY 586 CONFLICT SEQADV 6WBQ ARG A 593 UNP F1QCV2 GLY 593 CONFLICT SEQADV 6WBQ ARG A 596 UNP F1QCV2 THR 596 CONFLICT SEQADV 6WBQ MET A 613 UNP F1QCV2 THR 613 CONFLICT SEQADV 6WBQ PRO A 646 UNP F1QCV2 LEU 646 CONFLICT SEQADV 6WBQ 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 N9W A 701 25 HET EDO A 702 4 HET EDO A 703 4 HET EDO A 704 4 HET EDO A 705 4 HET EDO A 706 4 HET K A 707 1 HET K A 708 1 HET PO4 A 709 5 HET PO4 A 710 5 HET PO4 A 711 5 HET ZN A 712 1 HETNAM N9W 4-[(2-METHYL-3,4-DIHYDRO-1~{H}-PYRIDO[4,3-B]INDOL-5- HETNAM 2 N9W YL)METHYL]-~{N}-OXIDANYL-BENZAMIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM K POTASSIUM ION HETNAM PO4 PHOSPHATE ION HETNAM ZN ZINC ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 N9W C20 H21 N3 O2 FORMUL 3 EDO 5(C2 H6 O2) FORMUL 8 K 2(K 1+) FORMUL 10 PO4 3(O4 P 3-) FORMUL 13 ZN ZN 2+ FORMUL 14 HOH *194(H2 O) HELIX 1 AA1 ASP A 10 ARG A 15 5 6 HELIX 2 AA2 GLU A 24 VAL A 29 5 6 HELIX 3 AA3 PRO A 30 HIS A 43 1 14 HELIX 4 AA4 LEU A 45 CYS A 49 5 5 HELIX 5 AA5 THR A 58 LEU A 63 1 6 HELIX 6 AA6 SER A 67 GLN A 76 1 10 HELIX 7 AA7 THR A 77 MET A 80 5 4 HELIX 8 AA8 ASN A 81 LYS A 90 1 10 HELIX 9 AA9 ASN A 100 LYS A 121 1 22 HELIX 10 AB1 ASN A 150 ASN A 164 1 15 HELIX 11 AB2 GLY A 178 GLU A 186 1 9 HELIX 12 AB3 LEU A 208 ASP A 212 5 5 HELIX 13 AB4 LYS A 218 SER A 222 5 5 HELIX 14 AB5 THR A 236 VAL A 247 1 12 HELIX 15 AB6 VAL A 247 ASP A 256 1 10 HELIX 16 AB7 GLU A 282 MET A 292 1 11 HELIX 17 AB8 PRO A 293 GLY A 297 5 5 HELIX 18 AB9 ASN A 308 LEU A 324 1 17 HELIX 19 AC1 CYS A 338 SER A 353 1 16 HELIX 20 AC2 SER A 354 TYR A 355 5 2 HELIX 21 AC3 TRP A 356 LYS A 360 5 5 HELIX 22 AC4 SER A 438 PHE A 453 1 16 HELIX 23 AC5 ASP A 458 ARG A 477 1 20 HELIX 24 AC6 ASP A 490 THR A 504 1 15 HELIX 25 AC7 SER A 556 LEU A 568 1 13 HELIX 26 AC8 LEU A 568 ASN A 577 1 10 HELIX 27 AC9 VAL A 597 GLN A 606 1 10 HELIX 28 AD1 GLY A 607 GLY A 611 5 5 HELIX 29 AD2 ASP A 621 SER A 633 1 13 HELIX 30 AD3 LYS A 647 GLN A 662 1 16 HELIX 31 AD4 TRP A 665 ARG A 669 5 5 SHEET 1 AA1 8 LYS A 50 ALA A 51 0 SHEET 2 AA1 8 SER A 5 ILE A 8 1 N LEU A 7 O LYS A 50 SHEET 3 AA1 8 ASN A 126 ALA A 129 1 O MET A 128 N ILE A 8 SHEET 4 AA1 8 MET A 299 LEU A 303 1 O VAL A 301 N GLY A 127 SHEET 5 AA1 8 LEU A 259 ALA A 264 1 N VAL A 260 O CYS A 300 SHEET 6 AA1 8 ILE A 168 ASP A 172 1 N LEU A 169 O ILE A 261 SHEET 7 AA1 8 VAL A 191 ARG A 198 1 O LEU A 192 N ILE A 170 SHEET 8 AA1 8 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 VAL A 515 O ILE A 584 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 SSBOND 1 CYS A 543 CYS A 543 1555 4555 2.08 LINK O ASP A 172 K K A 707 1555 1555 2.97 LINK OD2 ASP A 172 K K A 707 1555 1555 2.71 LINK O ASP A 174 K K A 707 1555 1555 2.69 LINK OD2 ASP A 174 ZN ZN A 712 1555 1555 1.95 LINK O HIS A 176 K K A 707 1555 1555 2.68 LINK ND1 HIS A 176 ZN ZN A 712 1555 1555 2.23 LINK O PHE A 185 K K A 708 1555 1555 2.60 LINK O ASP A 188 K K A 708 1555 1555 2.70 LINK O VAL A 191 K K A 708 1555 1555 2.48 LINK OG SER A 195 K K A 707 1555 1555 2.83 LINK O TRP A 196 K K A 707 1555 1555 2.64 LINK O PHE A 224 K K A 708 1555 1555 3.14 LINK OD2 ASP A 267 ZN ZN A 712 1555 1555 2.06 LINK O2 N9W A 701 ZN ZN A 712 1555 1555 2.09 LINK N1 N9W A 701 ZN ZN A 712 1555 1555 2.62 LINK O1 N9W A 701 ZN ZN A 712 1555 1555 2.11 LINK K K A 708 O HOH A 862 1555 1555 3.50 LINK K K A 708 O HOH A 887 1555 1555 2.50 LINK K K A 708 O HOH A 971 1555 1555 2.41 CISPEP 1 ARG A 132 PRO A 133 0 0.54 CISPEP 2 TRP A 205 PRO A 206 0 5.62 CISPEP 3 GLU A 505 PRO A 506 0 1.47 SITE 1 AC1 13 GLU A 24 ALA A 94 HIS A 136 HIS A 137 SITE 2 AC1 13 GLY A 145 PHE A 146 ASP A 174 HIS A 176 SITE 3 AC1 13 TRP A 205 ASP A 267 GLU A 274 TYR A 307 SITE 4 AC1 13 ZN A 712 SITE 1 AC2 9 ALA A 2 VAL A 119 ARG A 122 VAL A 124 SITE 2 AC2 9 ARG A 125 ALA A 296 LYS A 298 HOH A 818 SITE 3 AC2 9 HOH A 828 SITE 1 AC3 5 GLY A 4 SER A 5 ARG A 125 LEU A 323 SITE 2 AC3 5 HOH A 962 SITE 1 AC4 4 GLU A 59 LEU A 63 GLU A 68 GLU A 72 SITE 1 AC5 3 ASN A 81 LYS A 360 HIS A 361 SITE 1 AC6 3 ARG A 198 GLU A 200 GLU A 276 SITE 1 AC7 5 ASP A 172 ASP A 174 HIS A 176 SER A 195 SITE 2 AC7 5 TRP A 196 SITE 1 AC8 6 PHE A 185 ASP A 188 VAL A 191 PHE A 224 SITE 2 AC8 6 HOH A 887 HOH A 971 SITE 1 AC9 10 GLN A 56 LYS A 106 HIS A 201 ASP A 212 SITE 2 AC9 10 TYR A 213 ASN A 231 HOH A 806 HOH A 813 SITE 3 AC9 10 HOH A 816 HOH A 916 SITE 1 AD1 7 LYS A 75 HIS A 201 ASN A 231 LYS A 232 SITE 2 AD1 7 SER A 340 GLU A 343 HOH A 913 SITE 1 AD2 4 HIS A 43 HIS A 321 LYS A 407 ARG A 408 SITE 1 AD3 4 ASP A 174 HIS A 176 ASP A 267 N9W A 701 CRYST1 80.630 80.630 246.811 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 0.012402 0.007160 0.000000 0.00000 SCALE2 0.000000 0.014321 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004052 0.00000