HEADER TRANSCRIPTION 14-NOV-14 4D6Q TITLE CRYSTAL STRUCTURE OF HUMAN JMJD2D IN COMPLEX WITH 2,4-PDCA COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JUMONJI DOMAIN, RESIDUES 1-342; COMPND 5 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, COMPND 6 JUMONJI DOMAIN-CONTAINING PROTEIN 2D, JMJD2D; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: 2,4-PYRIDINECARBOXYLIC ACID IS BOUND TO ACTIVE SITE NI COMPND 9 ATOM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION, KDM4D, FLJ10251, MGC141909, DEMETHYLASE/2OG, JUMONJI KEYWDS 2 DOMAIN CONTAINING 2D EXPDTA X-RAY DIFFRACTION AUTHOR T.KROJER,M.VOLLMAR,A.BRADLEY,L.CRAWLEY,A.SZYKOWSKA,N.BURGESS-BROWN, AUTHOR 2 C.GILEADI,C.JOHANSSON,U.OPPERMANN,C.BOUNTRA,C.H.ARROWSMITH, AUTHOR 3 A.EDWARDS,F.VON DELFT REVDAT 2 24-JAN-18 4D6Q 1 JRNL REVDAT 1 24-DEC-14 4D6Q 0 JRNL AUTH T.KROJER,M.VOLLMAR,A.BRADLEY,L.CRAWLEY,A.SZYKOWSKA, JRNL AUTH 2 N.BURGESS-BROWN,C.GILEADI,C.JOHANSSON,U.OPPERMANN,C.BOUNTRA, JRNL AUTH 3 C.H.ARROWSMITH,A.EDWARDS,F.VON DELFT JRNL TITL CRYSTAL STRUCTURE OF HUMAN JMJD2D IN COMPLEX WITH 2,4-PDCA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.890 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 99584 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 : 0.161 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5006 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 33.4459 - 4.0137 1.00 3482 155 0.1519 0.1766 REMARK 3 2 4.0137 - 3.1866 0.99 3275 168 0.1359 0.1579 REMARK 3 3 3.1866 - 2.7840 1.00 3198 195 0.1516 0.1754 REMARK 3 4 2.7840 - 2.5296 1.00 3223 166 0.1523 0.1859 REMARK 3 5 2.5296 - 2.3483 1.00 3157 200 0.1405 0.1512 REMARK 3 6 2.3483 - 2.2099 1.00 3208 152 0.1369 0.1603 REMARK 3 7 2.2099 - 2.0993 1.00 3191 141 0.1291 0.1564 REMARK 3 8 2.0993 - 2.0079 1.00 3149 173 0.1194 0.1367 REMARK 3 9 2.0079 - 1.9306 1.00 3163 178 0.1184 0.1379 REMARK 3 10 1.9306 - 1.8640 1.00 3143 168 0.1158 0.1378 REMARK 3 11 1.8640 - 1.8057 1.00 3131 163 0.1144 0.1518 REMARK 3 12 1.8057 - 1.7541 1.00 3116 178 0.1121 0.1367 REMARK 3 13 1.7541 - 1.7079 1.00 3152 169 0.1094 0.1424 REMARK 3 14 1.7079 - 1.6662 1.00 3144 149 0.1085 0.1405 REMARK 3 15 1.6662 - 1.6284 1.00 3150 161 0.1094 0.1321 REMARK 3 16 1.6284 - 1.5937 1.00 3120 155 0.1065 0.1516 REMARK 3 17 1.5937 - 1.5618 1.00 3127 156 0.1100 0.1562 REMARK 3 18 1.5618 - 1.5324 1.00 3115 174 0.1171 0.1459 REMARK 3 19 1.5324 - 1.5050 1.00 3128 171 0.1151 0.1699 REMARK 3 20 1.5050 - 1.4795 1.00 3124 155 0.1190 0.1624 REMARK 3 21 1.4795 - 1.4556 1.00 3121 165 0.1252 0.1584 REMARK 3 22 1.4556 - 1.4332 1.00 3106 177 0.1285 0.1654 REMARK 3 23 1.4332 - 1.4121 1.00 3093 167 0.1380 0.1563 REMARK 3 24 1.4121 - 1.3923 1.00 3125 166 0.1406 0.1644 REMARK 3 25 1.3923 - 1.3734 1.00 3094 178 0.1452 0.2004 REMARK 3 26 1.3734 - 1.3556 1.00 3109 173 0.1570 0.1897 REMARK 3 27 1.3556 - 1.3387 1.00 3095 148 0.1578 0.1828 REMARK 3 28 1.3387 - 1.3225 1.00 3117 186 0.1679 0.2028 REMARK 3 29 1.3225 - 1.3071 1.00 3061 175 0.1723 0.2283 REMARK 3 30 1.3071 - 1.2925 1.00 3161 144 0.1887 0.2249 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2993 REMARK 3 ANGLE : 1.079 4083 REMARK 3 CHIRALITY : 0.049 407 REMARK 3 PLANARITY : 0.006 550 REMARK 3 DIHEDRAL : 12.291 1110 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 4D6Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1290062313. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAY-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 : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PIXEL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 99689 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 33.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.68000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG3350 -- 0.1M HEPES PH 7.0 -- REMARK 280 0.25M AMMONIUM SULFATE 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 75.53000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.95500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.95500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 113.29500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.95500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.95500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.76500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.95500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.95500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 113.29500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.95500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.95500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.76500 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 75.53000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.8 KCAL/MOL 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 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 75.53000 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 A2217 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 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 ASP A 341 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 LYS A 58 CD CE NZ REMARK 470 GLU A 61 CD OE1 OE2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 GLU A 119 CD OE1 OE2 REMARK 470 ARG A 225 NE CZ NH1 NH2 REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 340 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2282 O HOH A 2283 2.10 REMARK 500 OD1 ASN A 202 O HOH A 2293 2.12 REMARK 500 O HOH A 2092 O HOH A 2377 2.14 REMARK 500 O HOH A 2153 O HOH A 2156 2.16 REMARK 500 OH TYR A 303 O HOH A 2377 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 186 -5.45 75.38 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 A2042 DISTANCE = 5.86 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1341 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 238 SG REMARK 620 2 HIS A 244 NE2 109.6 REMARK 620 3 CYS A 310 SG 116.5 109.7 REMARK 620 4 CYS A 312 SG 114.1 99.1 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A1342 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 194 OE2 REMARK 620 2 HIS A 192 NE2 98.6 REMARK 620 3 HIS A 280 NE2 89.4 84.5 REMARK 620 4 HOH A2287 O 87.4 174.1 96.1 REMARK 620 5 PD2 A1343 O22 97.2 84.6 168.0 94.2 REMARK 620 6 PD2 A1343 N1 162.0 97.8 99.5 76.2 77.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PD2 A 1343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1344 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1345 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1346 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1347 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1348 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1349 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D6R RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2D IN COMPLEX WITH N- OXALYLGLYCINE REMARK 900 AND BOUND O-TOLUENESULFONAMIDE REMARK 900 RELATED ID: 4D6S RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2D IN COMPLEX WITH N- OXALYLGLYCINE REMARK 900 AND BOUND 5,6-DIMETHYLBENZIMIDAZOLE DBREF 4D6Q A 1 342 UNP Q6B0I6 KDM4D_HUMAN 1 342 SEQADV 4D6Q SER A 0 UNP Q6B0I6 EXPRESSION TAG SEQRES 1 A 343 SER MET GLU THR MET LYS SER LYS ALA ASN CYS ALA GLN SEQRES 2 A 343 ASN PRO ASN CYS ASN ILE MET ILE PHE HIS PRO THR LYS SEQRES 3 A 343 GLU GLU PHE ASN ASP PHE ASP LYS TYR ILE ALA TYR MET SEQRES 4 A 343 GLU SER GLN GLY ALA HIS ARG ALA GLY LEU ALA LYS ILE SEQRES 5 A 343 ILE PRO PRO LYS GLU TRP LYS ALA ARG GLU THR TYR ASP SEQRES 6 A 343 ASN ILE SER GLU ILE LEU ILE ALA THR PRO LEU GLN GLN SEQRES 7 A 343 VAL ALA SER GLY ARG ALA GLY VAL PHE THR GLN TYR HIS SEQRES 8 A 343 LYS LYS LYS LYS ALA MET THR VAL GLY GLU TYR ARG HIS SEQRES 9 A 343 LEU ALA ASN SER LYS LYS TYR GLN THR PRO PRO HIS GLN SEQRES 10 A 343 ASN PHE GLU ASP LEU GLU ARG LYS TYR TRP LYS ASN ARG SEQRES 11 A 343 ILE TYR ASN SER PRO ILE TYR GLY ALA ASP ILE SER GLY SEQRES 12 A 343 SER LEU PHE ASP GLU ASN THR LYS GLN TRP ASN LEU GLY SEQRES 13 A 343 HIS LEU GLY THR ILE GLN ASP LEU LEU GLU LYS GLU CYS SEQRES 14 A 343 GLY VAL VAL ILE GLU GLY VAL ASN THR PRO TYR LEU TYR SEQRES 15 A 343 PHE GLY MET TRP LYS THR THR PHE ALA TRP HIS THR GLU SEQRES 16 A 343 ASP MET ASP LEU TYR SER ILE ASN TYR LEU HIS LEU GLY SEQRES 17 A 343 GLU PRO LYS THR TRP TYR VAL VAL PRO PRO GLU HIS GLY SEQRES 18 A 343 GLN ARG LEU GLU ARG LEU ALA ARG GLU LEU PHE PRO GLY SEQRES 19 A 343 SER SER ARG GLY CYS GLY ALA PHE LEU ARG HIS LYS VAL SEQRES 20 A 343 ALA LEU ILE SER PRO THR VAL LEU LYS GLU ASN GLY ILE SEQRES 21 A 343 PRO PHE ASN ARG ILE THR GLN GLU ALA GLY GLU PHE MET SEQRES 22 A 343 VAL THR PHE PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS SEQRES 23 A 343 GLY PHE ASN CYS ALA GLU ALA ILE ASN PHE ALA THR PRO SEQRES 24 A 343 ARG TRP ILE ASP TYR GLY LYS MET ALA SER GLN CYS SER SEQRES 25 A 343 CYS GLY GLU ALA ARG VAL THR PHE SER MET ASP ALA PHE SEQRES 26 A 343 VAL ARG ILE LEU GLN PRO GLU ARG TYR ASP LEU TRP LYS SEQRES 27 A 343 ARG GLY GLN ASP ARG HET ZN A1341 1 HET NI A1342 1 HET PD2 A1343 12 HET EDO A1344 4 HET EDO A1345 4 HET EDO A1346 4 HET EDO A1347 4 HET EDO A1348 4 HET SO4 A1349 5 HETNAM ZN ZINC ION HETNAM NI NICKEL (II) ION HETNAM PD2 PYRIDINE-2,4-DICARBOXYLIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 NI NI 2+ FORMUL 4 PD2 C7 H5 N O4 FORMUL 5 EDO 5(C2 H6 O2) FORMUL 10 SO4 O4 S 2- FORMUL 11 HOH *406(H2 O) HELIX 1 1 ASP A 30 GLN A 41 1 12 HELIX 2 2 GLY A 42 ALA A 46 5 5 HELIX 3 3 VAL A 98 ASN A 106 1 9 HELIX 4 4 ASN A 117 ARG A 129 1 13 HELIX 5 5 ILE A 130 ASN A 132 5 3 HELIX 6 6 THR A 159 GLY A 169 1 11 HELIX 7 7 GLU A 194 LEU A 198 5 5 HELIX 8 8 PRO A 216 GLU A 218 5 3 HELIX 9 9 HIS A 219 PHE A 231 1 13 HELIX 10 10 PHE A 231 CYS A 238 1 8 HELIX 11 11 ALA A 240 LYS A 245 5 6 HELIX 12 12 SER A 250 ASN A 257 1 8 HELIX 13 13 ARG A 299 ALA A 307 1 9 HELIX 14 14 SER A 320 GLN A 329 1 10 HELIX 15 15 GLN A 329 GLN A 340 1 12 SHEET 1 AA10 MET A 19 PHE A 21 0 SHEET 2 AA10 LEU A 48 ILE A 51 1 O LEU A 48 N MET A 19 SHEET 3 AA10 PHE A 271 THR A 274 -1 O PHE A 271 N ILE A 51 SHEET 4 AA10 TYR A 199 GLY A 207 -1 O SER A 200 N THR A 274 SHEET 5 AA10 ASN A 288 PHE A 295 -1 O CYS A 289 N HIS A 205 SHEET 6 AA10 TYR A 179 GLY A 183 -1 O TYR A 179 N ALA A 292 SHEET 7 AA10 ILE A 135 SER A 141 -1 O GLY A 137 N PHE A 182 SHEET 8 AA10 LEU A 75 ARG A 82 -1 O LEU A 75 N TYR A 136 SHEET 9 AA10 VAL A 85 LYS A 92 -1 O VAL A 85 N ARG A 82 SHEET 10 AA10 ALA A 247 ILE A 249 -1 O LEU A 248 N PHE A 86 SHEET 1 AB 2 LEU A 70 ILE A 71 0 SHEET 2 AB 2 MET A 96 THR A 97 -1 O MET A 96 N ILE A 71 SHEET 1 AC 4 THR A 188 HIS A 192 0 SHEET 2 AC 4 TYR A 279 ASN A 284 -1 O HIS A 280 N HIS A 192 SHEET 3 AC 4 LYS A 210 VAL A 215 -1 O THR A 211 N PHE A 283 SHEET 4 AC 4 ASN A 262 GLN A 266 -1 O ASN A 262 N VAL A 214 LINK ZN ZN A1341 SG CYS A 238 1555 1555 2.29 LINK ZN ZN A1341 NE2 HIS A 244 1555 1555 2.09 LINK ZN ZN A1341 SG CYS A 310 1555 1555 2.27 LINK ZN ZN A1341 SG CYS A 312 1555 1555 2.32 LINK NI NI A1342 OE2 GLU A 194 1555 1555 2.05 LINK NI NI A1342 NE2 HIS A 192 1555 1555 2.21 LINK NI NI A1342 NE2 HIS A 280 1555 1555 2.25 LINK NI NI A1342 O HOH A2287 1555 1555 2.21 LINK NI NI A1342 O22 PD2 A1343 1555 1555 2.11 LINK NI NI A1342 N1 PD2 A1343 1555 1555 2.10 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 PD2 A1343 SITE 2 AC2 5 HOH A2287 SITE 1 AC3 13 TYR A 136 PHE A 189 HIS A 192 GLU A 194 SITE 2 AC3 13 LYS A 210 LYS A 245 HIS A 280 NI A1342 SITE 3 AC3 13 EDO A1348 HOH A2234 HOH A2286 HOH A2287 SITE 4 AC3 13 HOH A2293 SITE 1 AC4 7 LYS A 150 GLN A 151 TRP A 152 ASN A 153 SITE 2 AC4 7 HIS A 156 HOH A2054 HOH A2055 SITE 1 AC5 5 PRO A 251 THR A 252 LYS A 255 ARG A 263 SITE 2 AC5 5 HOH A2405 SITE 1 AC6 6 PHE A 118 GLU A 122 ARG A 263 ILE A 264 SITE 2 AC6 6 THR A 265 HOH A2406 SITE 1 AC7 3 LYS A 124 LYS A 127 ASN A 128 SITE 1 AC8 8 TYR A 179 TYR A 181 GLU A 194 ALA A 292 SITE 2 AC8 8 PD2 A1343 HOH A2287 HOH A2293 HOH A2370 SITE 1 AC9 6 ARG A 60 GLU A 61 THR A 62 HOH A2120 SITE 2 AC9 6 HOH A2123 HOH A2264 CRYST1 71.910 71.910 151.060 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 0.013906 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013906 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006620 0.00000