HEADER HYDROLASE 03-MAR-23 8GD4 TITLE CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 6 CATALYTIC TITLE 2 DOMAIN 2 COMPLEXED WITH DMFO INHIBITOR 6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HDAC6 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN 2; COMPND 5 SYNONYM: HISTONE DEACETYLASE 6; 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: HDAC6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, HISTONE DEACETYLASE, INHIBITOR, METALLOHYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.R.WATSON,A.D.CRAIGIN,D.W.CHRISTIANSON REVDAT 3 25-OCT-23 8GD4 1 JRNL REVDAT 2 18-OCT-23 8GD4 1 JRNL REVDAT 1 04-OCT-23 8GD4 0 JRNL AUTH B.KONIG,P.R.WATSON,N.RESSING,A.D.CRAGIN,L.SCHAKER-HUBNER, JRNL AUTH 2 D.W.CHRISTIANSON,F.K.HANSEN JRNL TITL DIFLUOROMETHYL-1,3,4-OXADIAZOLES ARE SELECTIVE, JRNL TITL 2 MECHANISM-BASED, AND ESSENTIALLY IRREVERSIBLE INHIBITORS OF JRNL TITL 3 HISTONE DEACETYLASE 6 . JRNL REF J.MED.CHEM. V. 66 13821 2023 JRNL REFN ISSN 0022-2623 JRNL PMID 37782298 JRNL DOI 10.1021/ACS.JMEDCHEM.3C01345 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 45808 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.370 REMARK 3 FREE R VALUE TEST SET COUNT : 2003 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 29.5600 - 4.8100 0.99 3329 154 0.1687 0.1779 REMARK 3 2 4.8100 - 3.8200 1.00 3192 144 0.1473 0.1529 REMARK 3 3 3.8200 - 3.3400 1.00 3188 137 0.1633 0.2390 REMARK 3 4 3.3400 - 3.0300 1.00 3158 148 0.1985 0.2199 REMARK 3 5 3.0300 - 2.8100 1.00 3141 141 0.1927 0.2259 REMARK 3 6 2.8100 - 2.6500 1.00 3126 145 0.2032 0.2560 REMARK 3 7 2.6500 - 2.5200 1.00 3111 142 0.1915 0.2249 REMARK 3 8 2.5200 - 2.4100 1.00 3121 137 0.1924 0.2293 REMARK 3 9 2.4100 - 2.3100 1.00 3106 147 0.1848 0.2421 REMARK 3 10 2.3100 - 2.2300 1.00 3134 145 0.1990 0.2331 REMARK 3 11 2.2300 - 2.1600 1.00 3112 148 0.1983 0.2312 REMARK 3 12 2.1600 - 2.1000 1.00 3068 138 0.2038 0.3033 REMARK 3 13 2.1000 - 2.0500 1.00 3087 144 0.2185 0.2512 REMARK 3 14 2.0500 - 2.0000 0.94 2932 133 0.2319 0.2637 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.213 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.064 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.82 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 : 0.008 5663 REMARK 3 ANGLE : 0.956 7702 REMARK 3 CHIRALITY : 0.056 846 REMARK 3 PLANARITY : 0.012 1003 REMARK 3 DIHEDRAL : 25.476 791 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 : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 442 through 496 or REMARK 3 (resid 497 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 498 REMARK 3 through 508 or resid 510 through 561 or REMARK 3 (resid 562 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 563 REMARK 3 through 577 or (resid 578 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 579 through 633 or resid 635 REMARK 3 through 657 or (resid 658 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 659 or resid 661 through 671 or REMARK 3 (resid 672 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 673 REMARK 3 through 690 or resid 692 through 707 or REMARK 3 resid 709 through 735 or (resid 736 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 737 through 751 or REMARK 3 (resid 752 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 753 REMARK 3 through 754 or resid 756 through 769 or REMARK 3 (resid 770 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 774 REMARK 3 through 797 or resid 801)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 442 through 477 or REMARK 3 (resid 478 and (name N or name CA or name REMARK 3 C or name O or name CB or name CG )) or REMARK 3 resid 479 through 508 or resid 510 REMARK 3 through 517 or (resid 518 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 519 or (resid 520 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 521 through 523 or (resid 524 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB or name CG )) or resid 525 REMARK 3 through 527 or (resid 528 and (name N or REMARK 3 name CA or name C or name O or name CB or REMARK 3 name CG )) or resid 529 through 559 or REMARK 3 (resid 560 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 561 REMARK 3 through 633 or resid 635 through 659 or REMARK 3 resid 661 through 690 or resid 692 REMARK 3 through 707 or resid 709 through 754 or REMARK 3 resid 756 through 797 or resid 801)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8GD4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000272630. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-21 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 : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 1.20.1_4487 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 90179 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 36.216 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 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) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML HDAC6 PROTEIN, 0.04 M CITRIC REMARK 280 ACID, 0.06 M BIS-TRIS PROPANE (PH 5.0), 16% (W/V) POLYETHYLENE REMARK 280 GLYCOL 3,350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 37.40150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.23700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.18200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.23700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.40150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.18200 REMARK 290 SMTRY3 4 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 SER A 435 REMARK 465 ASN A 436 REMARK 465 ALA A 437 REMARK 465 GLY A 438 REMARK 465 GLY A 439 REMARK 465 SER A 440 REMARK 465 SER A 441 REMARK 465 ARG A 798 REMARK 465 SER B 435 REMARK 465 ASN B 436 REMARK 465 ALA B 437 REMARK 465 GLY B 438 REMARK 465 GLY B 439 REMARK 465 SER B 440 REMARK 465 SER B 441 REMARK 465 HIS B 771 REMARK 465 LEU B 772 REMARK 465 THR B 773 REMARK 465 ARG B 798 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 478 CD OE1 OE2 REMARK 470 GLU A 497 CD OE1 OE2 REMARK 470 LYS A 518 CG CD CE NZ REMARK 470 ARG A 520 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 523 CG OD1 ND2 REMARK 470 ARG A 524 CD NE CZ NH1 NH2 REMARK 470 GLU A 528 CD OE1 OE2 REMARK 470 GLN A 560 CG CD OE1 NE2 REMARK 470 ARG A 562 CD NE CZ NH1 NH2 REMARK 470 GLU A 602 CG CD OE1 OE2 REMARK 470 LYS A 672 CD CE NZ REMARK 470 HIS A 771 CB CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 788 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 497 CG CD OE1 OE2 REMARK 470 LYS B 518 CD CE NZ REMARK 470 ASN B 523 CG OD1 ND2 REMARK 470 GLN B 560 CD OE1 NE2 REMARK 470 ARG B 562 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 578 CG OD1 OD2 REMARK 470 GLU B 602 CG CD OE1 OE2 REMARK 470 LYS B 658 CG CD CE NZ REMARK 470 LYS B 672 CG CD CE NZ REMARK 470 ARG B 736 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 752 CG CD OE1 OE2 REMARK 470 ASP B 770 CG OD1 OD2 REMARK 470 ARG B 788 CG CD NE CZ NH1 NH2 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 SER A 531 61.81 64.83 REMARK 500 CYS A 581 141.59 -172.58 REMARK 500 THR A 600 -96.39 -124.92 REMARK 500 ALA A 641 50.38 -95.80 REMARK 500 LEU A 685 -60.08 -122.37 REMARK 500 GLN A 716 40.13 -141.06 REMARK 500 GLU A 742 -110.74 -114.92 REMARK 500 SER B 531 61.55 64.82 REMARK 500 CYS B 581 142.04 -171.71 REMARK 500 THR B 600 -96.34 -125.32 REMARK 500 ALA B 641 50.42 -97.45 REMARK 500 LEU B 685 -59.61 -123.57 REMARK 500 GLN B 716 40.04 -140.94 REMARK 500 GLU B 742 -109.93 -113.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 708 0.10 SIDE CHAIN 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 803 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 O REMARK 620 2 ASP A 610 OD1 69.5 REMARK 620 3 ASP A 612 O 96.4 93.9 REMARK 620 4 HIS A 614 O 160.1 91.4 78.8 REMARK 620 5 SER A 633 OG 86.4 110.9 154.2 106.4 REMARK 620 6 LEU A 634 O 80.0 142.6 67.9 115.1 87.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 612 OD1 REMARK 620 2 HIS A 614 ND1 107.2 REMARK 620 3 ASP A 705 OD2 109.2 99.5 REMARK 620 4 Z4I A 801 N05 114.3 95.6 126.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 804 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 623 O REMARK 620 2 ASP A 626 O 77.6 REMARK 620 3 VAL A 629 O 118.6 79.0 REMARK 620 4 TYR A 662 O 154.5 115.8 86.2 REMARK 620 5 HOH A 909 O 82.4 86.7 150.6 77.1 REMARK 620 6 HOH A 919 O 71.8 148.9 120.7 90.9 84.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 803 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 610 O REMARK 620 2 ASP B 610 OD1 71.6 REMARK 620 3 ASP B 612 O 99.2 98.1 REMARK 620 4 HIS B 614 O 161.7 90.3 80.2 REMARK 620 5 SER B 633 OG 85.1 112.5 148.7 105.1 REMARK 620 6 LEU B 634 O 79.5 145.9 68.6 116.6 82.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 612 OD1 REMARK 620 2 HIS B 614 ND1 109.7 REMARK 620 3 ASP B 705 OD2 112.1 99.4 REMARK 620 4 Z4I B 801 N05 113.7 96.5 122.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 804 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 623 O REMARK 620 2 ASP B 626 O 78.5 REMARK 620 3 VAL B 629 O 116.7 81.8 REMARK 620 4 TYR B 662 O 154.2 116.3 87.4 REMARK 620 5 HOH B 959 O 82.6 88.3 155.8 77.2 REMARK 620 6 HOH B 991 O 66.3 144.2 119.3 94.6 81.0 REMARK 620 N 1 2 3 4 5 DBREF 8GD4 A 440 798 UNP A7YT55 A7YT55_DANRE 288 646 DBREF 8GD4 B 440 798 UNP A7YT55 A7YT55_DANRE 288 646 SEQADV 8GD4 SER A 435 UNP A7YT55 EXPRESSION TAG SEQADV 8GD4 ASN A 436 UNP A7YT55 EXPRESSION TAG SEQADV 8GD4 ALA A 437 UNP A7YT55 EXPRESSION TAG SEQADV 8GD4 GLY A 438 UNP A7YT55 EXPRESSION TAG SEQADV 8GD4 GLY A 439 UNP A7YT55 EXPRESSION TAG SEQADV 8GD4 SER B 435 UNP A7YT55 EXPRESSION TAG SEQADV 8GD4 ASN B 436 UNP A7YT55 EXPRESSION TAG SEQADV 8GD4 ALA B 437 UNP A7YT55 EXPRESSION TAG SEQADV 8GD4 GLY B 438 UNP A7YT55 EXPRESSION TAG SEQADV 8GD4 GLY B 439 UNP A7YT55 EXPRESSION TAG SEQRES 1 A 364 SER ASN ALA GLY GLY SER SER PRO ILE THR GLY LEU VAL SEQRES 2 A 364 TYR ASP GLN ARG MET MET LEU HIS HIS ASN MET TRP ASP SEQRES 3 A 364 SER HIS HIS PRO GLU LEU PRO GLN ARG ILE SER ARG ILE SEQRES 4 A 364 PHE SER ARG HIS GLU GLU LEU ARG LEU LEU SER ARG CYS SEQRES 5 A 364 HIS ARG ILE PRO ALA ARG LEU ALA THR GLU GLU GLU LEU SEQRES 6 A 364 ALA LEU CYS HIS SER SER LYS HIS ILE SER ILE ILE LYS SEQRES 7 A 364 SER SER GLU HIS MET LYS PRO ARG ASP LEU ASN ARG LEU SEQRES 8 A 364 GLY ASP GLU TYR ASN SER ILE PHE ILE SER ASN GLU SER SEQRES 9 A 364 TYR THR CYS ALA LEU LEU ALA ALA GLY SER CYS PHE ASN SEQRES 10 A 364 SER ALA GLN ALA ILE LEU THR GLY GLN VAL ARG ASN ALA SEQRES 11 A 364 VAL ALA ILE VAL ARG PRO PRO GLY HIS HIS ALA GLU LYS SEQRES 12 A 364 ASP THR ALA CYS GLY PHE CYS PHE PHE ASN THR ALA ALA SEQRES 13 A 364 LEU THR ALA ARG TYR ALA GLN SER ILE THR ARG GLU SER SEQRES 14 A 364 LEU ARG VAL LEU ILE VAL ASP TRP ASP VAL HIS HIS GLY SEQRES 15 A 364 ASN GLY THR GLN HIS ILE PHE GLU GLU ASP ASP SER VAL SEQRES 16 A 364 LEU TYR ILE SER LEU HIS ARG TYR GLU ASP GLY ALA PHE SEQRES 17 A 364 PHE PRO ASN SER GLU ASP ALA ASN TYR ASP LYS VAL GLY SEQRES 18 A 364 LEU GLY LYS GLY ARG GLY TYR ASN VAL ASN ILE PRO TRP SEQRES 19 A 364 ASN GLY GLY LYS MET GLY ASP PRO GLU TYR MET ALA ALA SEQRES 20 A 364 PHE HIS HIS LEU VAL MET PRO ILE ALA ARG GLU PHE ALA SEQRES 21 A 364 PRO GLU LEU VAL LEU VAL SER ALA GLY PHE ASP ALA ALA SEQRES 22 A 364 ARG GLY ASP PRO LEU GLY GLY PHE GLN VAL THR PRO GLU SEQRES 23 A 364 GLY TYR ALA HIS LEU THR HIS GLN LEU MET SER LEU ALA SEQRES 24 A 364 ALA GLY ARG VAL LEU ILE ILE LEU GLU GLY GLY TYR ASN SEQRES 25 A 364 LEU THR SER ILE SER GLU SER MET SER MET CYS THR SER SEQRES 26 A 364 MET LEU LEU GLY ASP SER PRO PRO SER LEU ASP HIS LEU SEQRES 27 A 364 THR PRO LEU LYS THR SER ALA THR VAL SER ILE ASN ASN SEQRES 28 A 364 VAL LEU ARG ALA HIS ALA PRO PHE TRP SER SER LEU ARG SEQRES 1 B 364 SER ASN ALA GLY GLY SER SER PRO ILE THR GLY LEU VAL SEQRES 2 B 364 TYR ASP GLN ARG MET MET LEU HIS HIS ASN MET TRP ASP SEQRES 3 B 364 SER HIS HIS PRO GLU LEU PRO GLN ARG ILE SER ARG ILE SEQRES 4 B 364 PHE SER ARG HIS GLU GLU LEU ARG LEU LEU SER ARG CYS SEQRES 5 B 364 HIS ARG ILE PRO ALA ARG LEU ALA THR GLU GLU GLU LEU SEQRES 6 B 364 ALA LEU CYS HIS SER SER LYS HIS ILE SER ILE ILE LYS SEQRES 7 B 364 SER SER GLU HIS MET LYS PRO ARG ASP LEU ASN ARG LEU SEQRES 8 B 364 GLY ASP GLU TYR ASN SER ILE PHE ILE SER ASN GLU SER SEQRES 9 B 364 TYR THR CYS ALA LEU LEU ALA ALA GLY SER CYS PHE ASN SEQRES 10 B 364 SER ALA GLN ALA ILE LEU THR GLY GLN VAL ARG ASN ALA SEQRES 11 B 364 VAL ALA ILE VAL ARG PRO PRO GLY HIS HIS ALA GLU LYS SEQRES 12 B 364 ASP THR ALA CYS GLY PHE CYS PHE PHE ASN THR ALA ALA SEQRES 13 B 364 LEU THR ALA ARG TYR ALA GLN SER ILE THR ARG GLU SER SEQRES 14 B 364 LEU ARG VAL LEU ILE VAL ASP TRP ASP VAL HIS HIS GLY SEQRES 15 B 364 ASN GLY THR GLN HIS ILE PHE GLU GLU ASP ASP SER VAL SEQRES 16 B 364 LEU TYR ILE SER LEU HIS ARG TYR GLU ASP GLY ALA PHE SEQRES 17 B 364 PHE PRO ASN SER GLU ASP ALA ASN TYR ASP LYS VAL GLY SEQRES 18 B 364 LEU GLY LYS GLY ARG GLY TYR ASN VAL ASN ILE PRO TRP SEQRES 19 B 364 ASN GLY GLY LYS MET GLY ASP PRO GLU TYR MET ALA ALA SEQRES 20 B 364 PHE HIS HIS LEU VAL MET PRO ILE ALA ARG GLU PHE ALA SEQRES 21 B 364 PRO GLU LEU VAL LEU VAL SER ALA GLY PHE ASP ALA ALA SEQRES 22 B 364 ARG GLY ASP PRO LEU GLY GLY PHE GLN VAL THR PRO GLU SEQRES 23 B 364 GLY TYR ALA HIS LEU THR HIS GLN LEU MET SER LEU ALA SEQRES 24 B 364 ALA GLY ARG VAL LEU ILE ILE LEU GLU GLY GLY TYR ASN SEQRES 25 B 364 LEU THR SER ILE SER GLU SER MET SER MET CYS THR SER SEQRES 26 B 364 MET LEU LEU GLY ASP SER PRO PRO SER LEU ASP HIS LEU SEQRES 27 B 364 THR PRO LEU LYS THR SER ALA THR VAL SER ILE ASN ASN SEQRES 28 B 364 VAL LEU ARG ALA HIS ALA PRO PHE TRP SER SER LEU ARG HET Z4I A 801 23 HET ZN A 802 1 HET K A 803 1 HET K A 804 1 HET Z4I B 801 23 HET ZN B 802 1 HET K B 803 1 HET K B 804 1 HETNAM Z4I 2-(BENZYLAMINO)-N'-(DIFLUOROACETYL)PYRIMIDINE-5- HETNAM 2 Z4I CARBOHYDRAZIDE HETNAM ZN ZINC ION HETNAM K POTASSIUM ION FORMUL 3 Z4I 2(C14 H13 F2 N5 O2) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 K 4(K 1+) FORMUL 11 HOH *424(H2 O) HELIX 1 AA1 ASP A 449 HIS A 455 5 7 HELIX 2 AA2 PRO A 467 LEU A 480 1 14 HELIX 3 AA3 LEU A 482 CYS A 486 5 5 HELIX 4 AA4 THR A 495 ALA A 500 1 6 HELIX 5 AA5 SER A 504 SER A 514 1 11 HELIX 6 AA6 GLU A 515 MET A 517 5 3 HELIX 7 AA7 LYS A 518 GLU A 528 1 11 HELIX 8 AA8 GLU A 537 THR A 558 1 22 HELIX 9 AA9 ASN A 587 ILE A 599 1 13 HELIX 10 AB1 GLY A 616 GLU A 624 1 9 HELIX 11 AB2 GLU A 638 ALA A 641 5 4 HELIX 12 AB3 SER A 646 ASN A 650 5 5 HELIX 13 AB4 LEU A 656 ARG A 660 5 5 HELIX 14 AB5 GLY A 674 LEU A 685 1 12 HELIX 15 AB6 LEU A 685 ALA A 694 1 10 HELIX 16 AB7 THR A 718 MET A 730 1 13 HELIX 17 AB8 SER A 731 GLY A 735 5 5 HELIX 18 AB9 ASN A 746 LEU A 762 1 17 HELIX 19 AC1 LYS A 776 ALA A 791 1 16 HELIX 20 AC2 ASP B 449 HIS B 455 5 7 HELIX 21 AC3 PRO B 467 LEU B 480 1 14 HELIX 22 AC4 LEU B 482 CYS B 486 5 5 HELIX 23 AC5 THR B 495 ALA B 500 1 6 HELIX 24 AC6 SER B 504 SER B 514 1 11 HELIX 25 AC7 GLU B 515 MET B 517 5 3 HELIX 26 AC8 LYS B 518 ASP B 527 1 10 HELIX 27 AC9 GLU B 537 THR B 558 1 22 HELIX 28 AD1 ASN B 587 ILE B 599 1 13 HELIX 29 AD2 GLY B 616 GLU B 624 1 9 HELIX 30 AD3 GLU B 638 ALA B 641 5 4 HELIX 31 AD4 SER B 646 ASN B 650 5 5 HELIX 32 AD5 LEU B 656 ARG B 660 5 5 HELIX 33 AD6 GLY B 674 LEU B 685 1 12 HELIX 34 AD7 LEU B 685 ALA B 694 1 10 HELIX 35 AD8 THR B 718 MET B 730 1 13 HELIX 36 AD9 SER B 731 GLY B 735 5 5 HELIX 37 AE1 ASN B 746 LEU B 762 1 17 HELIX 38 AE2 LYS B 776 ALA B 791 1 16 SHEET 1 AA1 8 HIS A 487 ARG A 488 0 SHEET 2 AA1 8 THR A 444 VAL A 447 1 N THR A 444 O HIS A 487 SHEET 3 AA1 8 ASN A 563 ALA A 566 1 O ASN A 563 N GLY A 445 SHEET 4 AA1 8 VAL A 737 LEU A 741 1 O ILE A 739 N ALA A 566 SHEET 5 AA1 8 LEU A 697 ALA A 702 1 N VAL A 700 O ILE A 740 SHEET 6 AA1 8 VAL A 606 ASP A 610 1 N LEU A 607 O LEU A 699 SHEET 7 AA1 8 VAL A 629 ARG A 636 1 O ILE A 632 N ASP A 610 SHEET 8 AA1 8 ASN A 663 TRP A 668 1 O TRP A 668 N HIS A 635 SHEET 1 AA2 8 HIS B 487 ARG B 488 0 SHEET 2 AA2 8 THR B 444 VAL B 447 1 N THR B 444 O HIS B 487 SHEET 3 AA2 8 ASN B 563 ALA B 566 1 O ASN B 563 N GLY B 445 SHEET 4 AA2 8 VAL B 737 LEU B 741 1 O ILE B 739 N ALA B 566 SHEET 5 AA2 8 LEU B 697 ALA B 702 1 N VAL B 698 O LEU B 738 SHEET 6 AA2 8 VAL B 606 ASP B 610 1 N LEU B 607 O LEU B 699 SHEET 7 AA2 8 VAL B 629 ARG B 636 1 O ILE B 632 N ASP B 610 SHEET 8 AA2 8 ASN B 663 TRP B 668 1 O VAL B 664 N TYR B 631 LINK O ASP A 610 K K A 803 1555 1555 2.82 LINK OD1 ASP A 610 K K A 803 1555 1555 2.82 LINK OD1 ASP A 612 ZN ZN A 802 1555 1555 2.02 LINK O ASP A 612 K K A 803 1555 1555 2.67 LINK ND1 HIS A 614 ZN ZN A 802 1555 1555 2.15 LINK O HIS A 614 K K A 803 1555 1555 2.69 LINK O PHE A 623 K K A 804 1555 1555 2.61 LINK O ASP A 626 K K A 804 1555 1555 2.79 LINK O VAL A 629 K K A 804 1555 1555 2.72 LINK OG SER A 633 K K A 803 1555 1555 2.71 LINK O LEU A 634 K K A 803 1555 1555 2.63 LINK O TYR A 662 K K A 804 1555 1555 2.78 LINK OD2 ASP A 705 ZN ZN A 802 1555 1555 2.04 LINK N05 Z4I A 801 ZN ZN A 802 1555 1555 2.02 LINK K K A 804 O HOH A 909 1555 1555 2.73 LINK K K A 804 O HOH A 919 1555 1555 3.22 LINK O ASP B 610 K K B 803 1555 1555 2.79 LINK OD1 ASP B 610 K K B 803 1555 1555 2.76 LINK OD1 ASP B 612 ZN ZN B 802 1555 1555 1.98 LINK O ASP B 612 K K B 803 1555 1555 2.59 LINK ND1 HIS B 614 ZN ZN B 802 1555 1555 2.14 LINK O HIS B 614 K K B 803 1555 1555 2.74 LINK O PHE B 623 K K B 804 1555 1555 2.66 LINK O ASP B 626 K K B 804 1555 1555 2.87 LINK O VAL B 629 K K B 804 1555 1555 2.64 LINK OG SER B 633 K K B 803 1555 1555 2.90 LINK O LEU B 634 K K B 803 1555 1555 2.63 LINK O TYR B 662 K K B 804 1555 1555 2.84 LINK OD2 ASP B 705 ZN ZN B 802 1555 1555 2.05 LINK N05 Z4I B 801 ZN ZN B 802 1555 1555 1.99 LINK K K B 804 O HOH B 959 1555 1555 2.76 LINK K K B 804 O HOH B 991 1555 1555 3.11 CISPEP 1 ARG A 569 PRO A 570 0 -3.32 CISPEP 2 PHE A 643 PRO A 644 0 6.76 CISPEP 3 ARG B 569 PRO B 570 0 -3.43 CISPEP 4 PHE B 643 PRO B 644 0 6.24 CRYST1 74.803 92.364 96.474 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013368 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010827 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010365 0.00000 MTRIX1 1 -0.999958 -0.005369 -0.007441 74.76696 1 MTRIX2 1 -0.005446 0.999931 0.010417 0.09183 1 MTRIX3 1 0.007384 0.010458 -0.999918 22.05143 1