HEADER OXIDOREDUCTASE 07-FEB-17 5PHK TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF JMJD2D IN TITLE 2 COMPLEX WITH N09720A COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4D; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, COMPND 5 JUMONJI DOMAIN-CONTAINING PROTEIN 2D; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDM4D, JHDM3D, JMJD2D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PANDDA, SGC - DIAMOND I04-1 FRAGMENT SCREENING, JMJ DOMAIN, KEYWDS 2 EPIGENETICS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR N.M.PEARCE,T.KROJER,R.TALON,A.R.BRADLEY,M.FAIRHEAD,R.SETHI,N.WRIGHT, AUTHOR 2 E.MACLEAN,P.COLLINS,J.BRANDAO-NETO,A.DOUANGAMATH,Z.RENJIE,A.DIAS, AUTHOR 3 M.VOLLMAR,J.NG,A.SZYKOWSKA,N.BURGESS-BROWN,P.E.BRENNAN,O.COX, AUTHOR 4 U.OPPERMANN,C.BOUNTRA,C.H.ARROWSMITH,A.EDWARDS,F.VON DELFT REVDAT 4 06-MAR-24 5PHK 1 LINK REVDAT 3 04-OCT-17 5PHK 1 REMARK REVDAT 2 27-SEP-17 5PHK 1 JRNL REMARK REVDAT 1 15-MAR-17 5PHK 0 JRNL AUTH N.M.PEARCE,T.KROJER,A.R.BRADLEY,P.COLLINS,R.P.NOWAK,R.TALON, JRNL AUTH 2 B.D.MARSDEN,S.KELM,J.SHI,C.M.DEANE,F.VON DELFT JRNL TITL A MULTI-CRYSTAL METHOD FOR EXTRACTING OBSCURED JRNL TITL 2 CRYSTALLOGRAPHIC STATES FROM CONVENTIONALLY UNINTERPRETABLE JRNL TITL 3 ELECTRON DENSITY. JRNL REF NAT COMMUN V. 8 15123 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 28436492 JRNL DOI 10.1038/NCOMMS15123 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1682 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 107688 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.136 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 5302 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 29.4492 - 3.8824 1.00 3779 182 0.1537 0.1698 REMARK 3 2 3.8824 - 3.0826 1.00 3576 182 0.1357 0.1729 REMARK 3 3 3.0826 - 2.6933 1.00 3525 190 0.1438 0.1930 REMARK 3 4 2.6933 - 2.4471 1.00 3511 179 0.1411 0.1607 REMARK 3 5 2.4471 - 2.2718 1.00 3487 181 0.1364 0.1604 REMARK 3 6 2.2718 - 2.1379 1.00 3490 148 0.1247 0.1585 REMARK 3 7 2.1379 - 2.0309 1.00 3465 161 0.1202 0.1428 REMARK 3 8 2.0309 - 1.9425 1.00 3426 189 0.1171 0.1422 REMARK 3 9 1.9425 - 1.8677 1.00 3456 190 0.1147 0.1429 REMARK 3 10 1.8677 - 1.8033 1.00 3432 179 0.1129 0.1334 REMARK 3 11 1.8033 - 1.7469 1.00 3395 192 0.1127 0.1352 REMARK 3 12 1.7469 - 1.6970 1.00 3452 171 0.1090 0.1304 REMARK 3 13 1.6970 - 1.6523 1.00 3414 172 0.1092 0.1551 REMARK 3 14 1.6523 - 1.6120 1.00 3451 175 0.1098 0.1471 REMARK 3 15 1.6120 - 1.5753 1.00 3394 176 0.1087 0.1505 REMARK 3 16 1.5753 - 1.5418 1.00 3437 166 0.1089 0.1375 REMARK 3 17 1.5418 - 1.5110 1.00 3388 187 0.1107 0.1435 REMARK 3 18 1.5110 - 1.4825 1.00 3400 180 0.1119 0.1479 REMARK 3 19 1.4825 - 1.4560 1.00 3382 185 0.1162 0.1690 REMARK 3 20 1.4560 - 1.4313 1.00 3385 190 0.1219 0.1523 REMARK 3 21 1.4313 - 1.4082 1.00 3388 184 0.1289 0.1729 REMARK 3 22 1.4082 - 1.3866 1.00 3381 193 0.1363 0.1734 REMARK 3 23 1.3866 - 1.3662 1.00 3395 162 0.1426 0.1686 REMARK 3 24 1.3662 - 1.3469 1.00 3408 170 0.1509 0.1835 REMARK 3 25 1.3469 - 1.3287 1.00 3374 184 0.1622 0.2095 REMARK 3 26 1.3287 - 1.3115 0.99 3375 173 0.1781 0.1876 REMARK 3 27 1.3115 - 1.2951 0.98 3294 175 0.1882 0.2325 REMARK 3 28 1.2951 - 1.2795 0.97 3290 164 0.2097 0.2294 REMARK 3 29 1.2795 - 1.2646 0.95 3211 165 0.2281 0.2151 REMARK 3 30 1.2646 - 1.2504 0.89 3025 157 0.2487 0.2740 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.00 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 3149 REMARK 3 ANGLE : 1.088 4306 REMARK 3 CHIRALITY : 0.050 426 REMARK 3 PLANARITY : 0.006 570 REMARK 3 DIHEDRAL : 12.793 1210 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 5PHK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1001400668. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.97630 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 107796 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 29.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.66000 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 4D6R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG3350 -- 0.1M HEPES PH 7.0 -- REMARK 280 0.25M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.44000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.75100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.75100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 113.16000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.75100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.75100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.72000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.75100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.75100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 113.16000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.75100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.75100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.72000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.44000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 828 LIES ON A SPECIAL POSITION. 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 -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 SER A -14 REMARK 465 SER A -13 REMARK 465 GLY A -12 REMARK 465 VAL A -11 REMARK 465 ASP A -10 REMARK 465 LEU A -9 REMARK 465 GLY A -8 REMARK 465 THR A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 THR A 3 REMARK 465 MET A 4 REMARK 465 LYS A 5 REMARK 465 SER A 6 REMARK 465 LYS A 7 REMARK 465 ALA A 8 REMARK 465 ASN A 9 REMARK 465 CYS A 10 REMARK 465 ARG A 342 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 61 CG CD OE1 OE2 REMARK 470 LYS A 92 NZ REMARK 470 ARG A 225 NE CZ NH1 NH2 REMARK 470 LYS A 255 CD CE NZ REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 338 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 341 CG OD1 OD2 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 ASN A 176 88.80 -153.97 REMARK 500 LYS A 186 -4.92 75.66 REMARK 500 MET A 196 19.22 58.27 REMARK 500 MET A 196 19.67 57.81 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 A 936 DISTANCE = 6.03 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 YES C1CCC2C(C1)NC[NH]2 1.18 -10.14 REMARK 600 -10.14 C1CCC2C(C1)NC[NH]2 REMARK 600 4 - HIGH CONFIDENCE NONE REMARK 600 0.62 44.36 REMARK 600 2.4905395633616725 0.77900000000000003 REMARK 600 0.17199999999999999 0.20000000000000001 REMARK 600 0.2253079374249094 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 NI A 402 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 192 NE2 REMARK 620 2 GLU A 194 OE1 100.2 REMARK 620 3 HIS A 280 NE2 84.9 90.0 REMARK 620 4 OGA A 403 O1 166.7 93.1 96.0 REMARK 620 5 OGA A 403 O2' 90.7 167.6 96.9 75.9 REMARK 620 6 HOH A 645 O 88.9 87.0 172.6 90.9 87.4 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 CYS A 238 SG REMARK 620 2 HIS A 244 NE2 109.7 REMARK 620 3 CYS A 310 SG 114.7 109.8 REMARK 620 4 CYS A 312 SG 116.2 98.9 106.3 REMARK 620 N 1 2 3 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 NI A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OGA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BZI A 416 DBREF 5PHK A 1 342 UNP Q6B0I6 KDM4D_HUMAN 1 342 SEQADV 5PHK MET A -21 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK HIS A -20 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK HIS A -19 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK HIS A -18 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK HIS A -17 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK HIS A -16 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK HIS A -15 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK SER A -14 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK SER A -13 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK GLY A -12 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK VAL A -11 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK ASP A -10 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK LEU A -9 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK GLY A -8 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK THR A -7 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK GLU A -6 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK ASN A -5 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK LEU A -4 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK TYR A -3 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK PHE A -2 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK GLN A -1 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PHK SER A 0 UNP Q6B0I6 EXPRESSION TAG SEQRES 1 A 364 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 364 GLY THR GLU ASN LEU TYR PHE GLN SER MET GLU THR MET SEQRES 3 A 364 LYS SER LYS ALA ASN CYS ALA GLN ASN PRO ASN CYS ASN SEQRES 4 A 364 ILE MET ILE PHE HIS PRO THR LYS GLU GLU PHE ASN ASP SEQRES 5 A 364 PHE ASP LYS TYR ILE ALA TYR MET GLU SER GLN GLY ALA SEQRES 6 A 364 HIS ARG ALA GLY LEU ALA LYS ILE ILE PRO PRO LYS GLU SEQRES 7 A 364 TRP LYS ALA ARG GLU THR TYR ASP ASN ILE SER GLU ILE SEQRES 8 A 364 LEU ILE ALA THR PRO LEU GLN GLN VAL ALA SER GLY ARG SEQRES 9 A 364 ALA GLY VAL PHE THR GLN TYR HIS LYS LYS LYS LYS ALA SEQRES 10 A 364 MET THR VAL GLY GLU TYR ARG HIS LEU ALA ASN SER LYS SEQRES 11 A 364 LYS TYR GLN THR PRO PRO HIS GLN ASN PHE GLU ASP LEU SEQRES 12 A 364 GLU ARG LYS TYR TRP LYS ASN ARG ILE TYR ASN SER PRO SEQRES 13 A 364 ILE TYR GLY ALA ASP ILE SER GLY SER LEU PHE ASP GLU SEQRES 14 A 364 ASN THR LYS GLN TRP ASN LEU GLY HIS LEU GLY THR ILE SEQRES 15 A 364 GLN ASP LEU LEU GLU LYS GLU CYS GLY VAL VAL ILE GLU SEQRES 16 A 364 GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET TRP LYS SEQRES 17 A 364 THR THR PHE ALA TRP HIS THR GLU ASP MET ASP LEU TYR SEQRES 18 A 364 SER ILE ASN TYR LEU HIS LEU GLY GLU PRO LYS THR TRP SEQRES 19 A 364 TYR VAL VAL PRO PRO GLU HIS GLY GLN ARG LEU GLU ARG SEQRES 20 A 364 LEU ALA ARG GLU LEU PHE PRO GLY SER SER ARG GLY CYS SEQRES 21 A 364 GLY ALA PHE LEU ARG HIS LYS VAL ALA LEU ILE SER PRO SEQRES 22 A 364 THR VAL LEU LYS GLU ASN GLY ILE PRO PHE ASN ARG ILE SEQRES 23 A 364 THR GLN GLU ALA GLY GLU PHE MET VAL THR PHE PRO TYR SEQRES 24 A 364 GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN CYS ALA SEQRES 25 A 364 GLU ALA ILE ASN PHE ALA THR PRO ARG TRP ILE ASP TYR SEQRES 26 A 364 GLY LYS MET ALA SER GLN CYS SER CYS GLY GLU ALA ARG SEQRES 27 A 364 VAL THR PHE SER MET ASP ALA PHE VAL ARG ILE LEU GLN SEQRES 28 A 364 PRO GLU ARG TYR ASP LEU TRP LYS ARG GLY GLN ASP ARG HET ZN A 401 1 HET NI A 402 1 HET OGA A 403 10 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HET EDO A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET EDO A 411 8 HET SO4 A 412 5 HET SO4 A 413 5 HET SO4 A 414 5 HET SO4 A 415 5 HET BZI A 416 9 HETNAM ZN ZINC ION HETNAM NI NICKEL (II) ION HETNAM OGA N-OXALYLGLYCINE HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM BZI BENZIMIDAZOLE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 NI NI 2+ FORMUL 4 OGA C4 H5 N O5 FORMUL 5 EDO 8(C2 H6 O2) FORMUL 13 SO4 4(O4 S 2-) FORMUL 17 BZI C7 H6 N2 FORMUL 18 HOH *436(H2 O) HELIX 1 AA1 ASP A 30 GLN A 41 1 12 HELIX 2 AA2 GLY A 42 ALA A 46 5 5 HELIX 3 AA3 VAL A 98 ASN A 106 1 9 HELIX 4 AA4 ASN A 117 ARG A 129 1 13 HELIX 5 AA5 ILE A 130 ASN A 132 5 3 HELIX 6 AA6 THR A 159 GLY A 169 1 11 HELIX 7 AA7 GLU A 194 LEU A 198 5 5 HELIX 8 AA8 PRO A 216 GLU A 218 5 3 HELIX 9 AA9 HIS A 219 PHE A 231 1 13 HELIX 10 AB1 PHE A 231 CYS A 238 1 8 HELIX 11 AB2 ALA A 240 LYS A 245 5 6 HELIX 12 AB3 SER A 250 ASN A 257 1 8 HELIX 13 AB4 ARG A 299 ALA A 307 1 9 HELIX 14 AB5 SER A 320 GLN A 329 1 10 HELIX 15 AB6 GLN A 329 ASP A 341 1 13 SHEET 1 AA110 MET A 19 PHE A 21 0 SHEET 2 AA110 LEU A 48 ILE A 51 1 O LYS A 50 N PHE A 21 SHEET 3 AA110 PHE A 271 THR A 274 -1 O PHE A 271 N ILE A 51 SHEET 4 AA110 TYR A 199 GLY A 207 -1 N ASN A 202 O MET A 272 SHEET 5 AA110 ASN A 288 PHE A 295 -1 O GLU A 291 N TYR A 203 SHEET 6 AA110 TYR A 179 GLY A 183 -1 N TYR A 179 O ALA A 292 SHEET 7 AA110 ILE A 135 SER A 141 -1 N GLY A 137 O PHE A 182 SHEET 8 AA110 LEU A 75 GLY A 81 -1 N LEU A 75 O TYR A 136 SHEET 9 AA110 VAL A 85 LYS A 92 -1 O LYS A 91 N GLN A 76 SHEET 10 AA110 ALA A 247 ILE A 249 -1 O LEU A 248 N PHE A 86 SHEET 1 AA2 2 LEU A 70 ILE A 71 0 SHEET 2 AA2 2 MET A 96 THR A 97 -1 O MET A 96 N ILE A 71 SHEET 1 AA3 4 THR A 188 HIS A 192 0 SHEET 2 AA3 4 HIS A 280 ASN A 284 -1 O GLY A 282 N PHE A 189 SHEET 3 AA3 4 LYS A 210 VAL A 214 -1 N TYR A 213 O ALA A 281 SHEET 4 AA3 4 ASN A 262 GLN A 266 -1 O GLN A 266 N LYS A 210 LINK NE2 HIS A 192 NI NI A 402 1555 1555 2.25 LINK OE1 GLU A 194 NI NI A 402 1555 1555 2.03 LINK SG CYS A 238 ZN ZN A 401 1555 1555 2.29 LINK NE2 HIS A 244 ZN ZN A 401 1555 1555 2.09 LINK NE2 HIS A 280 NI NI A 402 1555 1555 2.19 LINK SG CYS A 310 ZN ZN A 401 1555 1555 2.27 LINK SG CYS A 312 ZN ZN A 401 1555 1555 2.32 LINK NI NI A 402 O1 AOGA A 403 1555 1555 2.14 LINK NI NI A 402 O2'AOGA A 403 1555 1555 2.12 LINK NI NI A 402 O HOH A 645 1555 1555 2.17 SITE 1 AC1 4 CYS A 238 HIS A 244 CYS A 310 CYS A 312 SITE 1 AC2 5 HIS A 192 GLU A 194 HIS A 280 OGA A 403 SITE 2 AC2 5 HOH A 645 SITE 1 AC3 13 TYR A 136 PHE A 189 HIS A 192 GLU A 194 SITE 2 AC3 13 SER A 200 ASN A 202 LYS A 210 HIS A 280 SITE 3 AC3 13 ALA A 292 NI A 402 EDO A 411 HOH A 645 SITE 4 AC3 13 HOH A 775 SITE 1 AC4 7 LYS A 150 GLN A 151 TRP A 152 ASN A 153 SITE 2 AC4 7 HIS A 156 HOH A 614 HOH A 728 SITE 1 AC5 4 PRO A 251 THR A 252 ARG A 263 HOH A 655 SITE 1 AC6 8 GLU A 224 ALA A 240 PHE A 241 LEU A 242 SITE 2 AC6 8 TYR A 279 SER A 308 HOH A 505 HOH A 547 SITE 1 AC7 7 ASP A 64 ASN A 65 ILE A 66 SER A 67 SITE 2 AC7 7 GLU A 68 ARG A 82 HOH A 679 SITE 1 AC8 4 PHE A 118 ILE A 264 THR A 265 HOH A 560 SITE 1 AC9 9 TRP A 57 LYS A 58 ALA A 59 TYR A 63 SITE 2 AC9 9 TYR A 203 HOH A 503 HOH A 506 HOH A 572 SITE 3 AC9 9 HOH A 685 SITE 1 AD1 6 SER A 80 THR A 87 CYS A 168 LYS A 305 SITE 2 AD1 6 HOH A 519 HOH A 783 SITE 1 AD2 9 TYR A 179 TYR A 181 GLU A 194 SER A 200 SITE 2 AD2 9 ALA A 292 ASN A 294 OGA A 403 HOH A 645 SITE 3 AD2 9 HOH A 665 SITE 1 AD3 5 ARG A 102 HIS A 103 ASN A 106 HOH A 515 SITE 2 AD3 5 HOH A 649 SITE 1 AD4 6 ARG A 60 GLU A 61 THR A 62 HOH A 504 SITE 2 AD4 6 HOH A 538 HOH A 554 SITE 1 AD5 4 ARG A 123 LYS A 124 LYS A 127 ASN A 128 SITE 1 AD6 6 PRO A 113 LYS A 124 ASN A 128 TRP A 185 SITE 2 AD6 6 LYS A 186 HOH A 627 SITE 1 AD7 13 ILE A 160 ASP A 195 ASN A 294 THR A 318 SITE 2 AD7 13 SER A 320 MET A 321 PHE A 324 HOH A 586 SITE 3 AD7 13 HOH A 653 HOH A 698 HOH A 765 HOH A 831 SITE 4 AD7 13 HOH A 843 CRYST1 71.502 71.502 150.880 90.00 90.00 90.00 P 43 21 2 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 0.013986 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013986 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006628 0.00000