HEADER OXIDOREDUCTASE 04-MAR-16 5FY5 TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX TITLE 2 WITH FUMARATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JMJC DOMAIN, RESIDUES 26-101 AND 374-770; COMPND 5 SYNONYM: CANCER/TESTIS ANTIGEN 31, CT31, HISTONE DEMETHYLASE JARID1B, COMPND 6 JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B, PLU-1, RETINOBLASTOMA - COMPND 7 BINDING PROTEIN 2 HOMOLOG 1, RBP2-H1, LYSINE-SPECIFIC DEMETHYLASE 5B, COMPND 8 LYSINE-SPECIFIC DEMETHYLASE 5B; COMPND 9 EC: 1.14.11.-; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PFB-LIC-BSE KEYWDS OXIDOREDUCTASE, JARID1B, PLU1, TCA INTERMEDIATE EXPDTA X-RAY DIFFRACTION AUTHOR R.NOWAK,V.SRIKANNATHASAN,C.JOHANSSON,C.GILEADI,K.KUPINSKA,C.STRAIN- AUTHOR 2 DAMERELL,A.SZYKOWSKA,F.VON DELFT,N.A.BURGESS-BROWN,C.H.ARROWSMITH, AUTHOR 3 C.BOUNTRA,A.M.EDWARDS,U.OPPERMANN REVDAT 4 10-JAN-24 5FY5 1 REMARK REVDAT 3 15-NOV-23 5FY5 1 REMARK LINK ATOM REVDAT 2 24-JAN-18 5FY5 1 AUTHOR JRNL REVDAT 1 22-MAR-17 5FY5 0 JRNL AUTH R.NOWAK,V.SRIKANNATHASAN,C.JOHANSSON,C.GILEADI,K.KUPINSKA, JRNL AUTH 2 C.STRAIN-DAMERELL,A.SZYKOWSKA,F.VON DELFT,N.A.BURGESS-BROWN, JRNL AUTH 3 C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS,U.OPPERMANN JRNL TITL CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B JRNL TITL 2 IN COMPLEX WITH FUMARATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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) : 2.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 33062 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1669 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 64.3056 - 5.6538 1.00 2847 136 0.1708 0.1777 REMARK 3 2 5.6538 - 4.4879 1.00 2689 140 0.1449 0.1613 REMARK 3 3 4.4879 - 3.9207 1.00 2626 148 0.1553 0.2069 REMARK 3 4 3.9207 - 3.5623 1.00 2626 139 0.1807 0.2451 REMARK 3 5 3.5623 - 3.3070 1.00 2614 131 0.2151 0.2542 REMARK 3 6 3.3070 - 3.1120 1.00 2599 128 0.2306 0.2731 REMARK 3 7 3.1120 - 2.9562 1.00 2568 142 0.2310 0.2957 REMARK 3 8 2.9562 - 2.8275 1.00 2565 151 0.2403 0.2963 REMARK 3 9 2.8275 - 2.7186 1.00 2566 141 0.2587 0.3197 REMARK 3 10 2.7186 - 2.6248 1.00 2580 135 0.2590 0.3202 REMARK 3 11 2.6248 - 2.5427 1.00 2562 132 0.2722 0.3358 REMARK 3 12 2.5427 - 2.4700 1.00 2551 146 0.2807 0.3286 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.009 3868 REMARK 3 ANGLE : 1.227 5250 REMARK 3 CHIRALITY : 0.048 557 REMARK 3 PLANARITY : 0.007 680 REMARK 3 DIHEDRAL : 14.659 1432 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 5FY5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1290066361. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.91732 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33120 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.470 REMARK 200 RESOLUTION RANGE LOW (A) : 64.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.80 REMARK 200 R MERGE (I) : 0.20000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.00 REMARK 200 R MERGE FOR SHELL (I) : 1.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: DIMPLE REMARK 200 STARTING MODEL: PDB ENTRY 5A3P REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 102.00000 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 51.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.50000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.50000 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 127.50000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 102.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 51.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.50000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 76.50000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 127.50000 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 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 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 MN MN A1768 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 LYS A 100 REMARK 465 LEU A 101 REMARK 465 GLY A 102 REMARK 465 GLY A 103 REMARK 465 GLY A 104 REMARK 465 GLY A 105 REMARK 465 ALA A 374 REMARK 465 GLY A 443 REMARK 465 LYS A 444 REMARK 465 SER A 754 REMARK 465 TYR A 755 REMARK 465 ASN A 756 REMARK 465 GLU A 757 REMARK 465 TRP A 758 REMARK 465 ALA A 759 REMARK 465 LEU A 760 REMARK 465 ASN A 761 REMARK 465 VAL A 762 REMARK 465 ASN A 763 REMARK 465 GLU A 764 REMARK 465 ALA A 765 REMARK 465 LEU A 766 REMARK 465 GLU A 767 REMARK 465 ALA A 768 REMARK 465 LYS A 769 REMARK 465 ILE A 770 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 86 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 432 CG CD CE NZ REMARK 470 GLU A 433 CG CD OE1 OE2 REMARK 470 PHE A 434 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 450 CG CD OE1 OE2 REMARK 470 GLU A 468 CG CD OE1 OE2 REMARK 470 GLN A 469 CG CD OE1 NE2 REMARK 470 LYS A 483 CG CD CE NZ 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 OG SER A 470 O HOH A 2027 2.19 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 TRP A 70 94.91 -62.89 REMARK 500 LEU A 90 76.25 -100.53 REMARK 500 ARG A 98 -70.73 -51.97 REMARK 500 ASP A 420 60.46 -117.74 REMARK 500 ALA A 473 -73.35 -55.13 REMARK 500 CYS A 480 -40.53 68.77 REMARK 500 PHE A 493 -12.06 74.02 REMARK 500 PRO A 546 0.21 -68.34 REMARK 500 ARG A 584 19.79 57.68 REMARK 500 PHE A 700 -52.40 -143.83 REMARK 500 PRO A 727 -8.96 -58.17 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 MN A1755 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 91 OD1 REMARK 620 2 THR A 416 O 150.2 REMARK 620 3 HOH A2015 O 99.7 109.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1756 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 499 NE2 REMARK 620 2 GLU A 501 OE2 97.2 REMARK 620 3 HIS A 587 NE2 86.9 83.1 REMARK 620 4 FUM A1766 O8 88.4 174.2 95.8 REMARK 620 5 HOH A2034 O 89.3 98.3 176.1 83.2 REMARK 620 6 HOH A2039 O 175.8 87.0 94.3 87.4 89.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1754 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 692 SG REMARK 620 2 CYS A 695 SG 104.2 REMARK 620 3 CYS A 715 SG 122.9 111.2 REMARK 620 4 HIS A 718 ND1 107.4 110.3 100.5 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 1754 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1755 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1756 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 1757 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1759 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1760 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1761 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1762 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1763 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1764 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1765 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FUM A 1766 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1767 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FXV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH N05859B REMARK 900 RELATED ID: 5FXW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH FUMARATE REMARK 900 RELATED ID: 5FXX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH OXALOACETATE REMARK 900 RELATED ID: 5FXZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH CITRATE REMARK 900 RELATED ID: 5FY0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH L-MALATE REMARK 900 RELATED ID: 5FY1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH N08619B REMARK 900 RELATED ID: 5FY4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH SUCCINATE REMARK 900 RELATED ID: 5FY7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH SUCCINATE REMARK 900 RELATED ID: 5FY8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH D- THREO- REMARK 900 ISOCITRATE REMARK 900 RELATED ID: 5FY9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH PYRUVATE REMARK 900 RELATED ID: 5FYB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MC1648 REMARK 900 RELATED ID: 5FYC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH SUCCINATE REMARK 900 RELATED ID: 5FYH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH FUMARATE REMARK 900 RELATED ID: 5FYI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH PYRUVATE REMARK 900 RELATED ID: 5FYM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH D-2-HYDROXYGLUTARATE REMARK 900 RELATED ID: 5FYS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH D-2-HYDROXYGLUTARATE REMARK 900 RELATED ID: 5FYT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH N09996A REMARK 900 RELATED ID: 5FYU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH N10042A REMARK 900 RELATED ID: 5FYV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH OXALOACETATE REMARK 900 RELATED ID: 5FYY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH N05798A REMARK 900 RELATED ID: 5FYZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH N10063A REMARK 900 RELATED ID: 5FZ0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH N11213A REMARK 900 RELATED ID: 5FZ1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH E48115B REMARK 900 RELATED ID: 5FZ3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH N08776B REMARK 900 RELATED ID: 5FZ4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH N10057A REMARK 900 RELATED ID: 5FZ6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MAYBRIDGE FRAGMENT N05859B ( LIGAND MODELLED BASED ON REMARK 900 PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING) REMARK 900 RELATED ID: 5FZ7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MAYBRIDGE FRAGMENT ETHYL 2- AMINO-4-THIOPHEN-2- REMARK 900 YLTHIOPHENE-3-CARBOXYLATE (N06131B ) (LIGAND MODELLED BASED ON REMARK 900 PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING) REMARK 900 RELATED ID: 5FZ8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MALATE DBREF 5FY5 A 26 101 UNP Q9UGL1 KDM5B_HUMAN 26 101 DBREF 5FY5 A 374 770 UNP Q9UGL1 KDM5B_HUMAN 374 770 SEQADV 5FY5 SER A 24 UNP Q9UGL1 EXPRESSION TAG SEQADV 5FY5 MET A 25 UNP Q9UGL1 EXPRESSION TAG SEQADV 5FY5 GLY A 102 UNP Q9UGL1 LINKER SEQADV 5FY5 GLY A 103 UNP Q9UGL1 LINKER SEQADV 5FY5 GLY A 104 UNP Q9UGL1 LINKER SEQADV 5FY5 GLY A 105 UNP Q9UGL1 LINKER SEQRES 1 A 479 SER MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU SEQRES 2 A 479 PRO SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE SEQRES 3 A 479 HIS LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS SEQRES 4 A 479 LYS VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA SEQRES 5 A 479 CYS ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN SEQRES 6 A 479 ARG LEU ASN GLU LEU GLU ALA GLN THR ARG VAL LYS LEU SEQRES 7 A 479 GLY GLY GLY GLY ALA ARG ASP TYR THR LEU ARG THR PHE SEQRES 8 A 479 GLY GLU MET ALA ASP ALA PHE LYS SER ASP TYR PHE ASN SEQRES 9 A 479 MET PRO VAL HIS MET VAL PRO THR GLU LEU VAL GLU LYS SEQRES 10 A 479 GLU PHE TRP ARG LEU VAL SER THR ILE GLU GLU ASP VAL SEQRES 11 A 479 THR VAL GLU TYR GLY ALA ASP ILE ALA SER LYS GLU PHE SEQRES 12 A 479 GLY SER GLY PHE PRO VAL ARG ASP GLY LYS ILE LYS LEU SEQRES 13 A 479 SER PRO GLU GLU GLU GLU TYR LEU ASP SER GLY TRP ASN SEQRES 14 A 479 LEU ASN ASN MET PRO VAL MET GLU GLN SER VAL LEU ALA SEQRES 15 A 479 HIS ILE THR ALA ASP ILE CYS GLY MET LYS LEU PRO TRP SEQRES 16 A 479 LEU TYR VAL GLY MET CYS PHE SER SER PHE CYS TRP HIS SEQRES 17 A 479 ILE GLU ASP HIS TRP SER TYR SER ILE ASN TYR LEU HIS SEQRES 18 A 479 TRP GLY GLU PRO LYS THR TRP TYR GLY VAL PRO GLY TYR SEQRES 19 A 479 ALA ALA GLU GLN LEU GLU ASN VAL MET LYS LYS LEU ALA SEQRES 20 A 479 PRO GLU LEU PHE VAL SER GLN PRO ASP LEU LEU HIS GLN SEQRES 21 A 479 LEU VAL THR ILE MET ASN PRO ASN THR LEU MET THR HIS SEQRES 22 A 479 GLU VAL PRO VAL TYR ARG THR ASN GLN CYS ALA GLY GLU SEQRES 23 A 479 PHE VAL ILE THR PHE PRO ARG ALA TYR HIS SER GLY PHE SEQRES 24 A 479 ASN GLN GLY PHE ASN PHE ALA GLU ALA VAL ASN PHE CYS SEQRES 25 A 479 THR VAL ASP TRP LEU PRO LEU GLY ARG GLN CYS VAL GLU SEQRES 26 A 479 HIS TYR ARG LEU LEU HIS ARG TYR CYS VAL PHE SER HIS SEQRES 27 A 479 ASP GLU MET ILE CYS LYS MET ALA SER LYS ALA ASP VAL SEQRES 28 A 479 LEU ASP VAL VAL VAL ALA SER THR VAL GLN LYS ASP MET SEQRES 29 A 479 ALA ILE MET ILE GLU ASP GLU LYS ALA LEU ARG GLU THR SEQRES 30 A 479 VAL ARG LYS LEU GLY VAL ILE ASP SER GLU ARG MET ASP SEQRES 31 A 479 PHE GLU LEU LEU PRO ASP ASP GLU ARG GLN CYS VAL LYS SEQRES 32 A 479 CYS LYS THR THR CYS PHE MET SER ALA ILE SER CYS SER SEQRES 33 A 479 CYS LYS PRO GLY LEU LEU VAL CYS LEU HIS HIS VAL LYS SEQRES 34 A 479 GLU LEU CYS SER CYS PRO PRO TYR LYS TYR LYS LEU ARG SEQRES 35 A 479 TYR ARG TYR THR LEU ASP ASP LEU TYR PRO MET MET ASN SEQRES 36 A 479 ALA LEU LYS LEU ARG ALA GLU SER TYR ASN GLU TRP ALA SEQRES 37 A 479 LEU ASN VAL ASN GLU ALA LEU GLU ALA LYS ILE HET ZN A1754 1 HET MN A1755 1 HET MN A1756 1 HET EPE A1757 15 HET EDO A1758 4 HET EDO A1759 4 HET EDO A1760 4 HET EDO A1761 4 HET EDO A1762 4 HET EDO A1763 4 HET EDO A1764 4 HET EDO A1765 4 HET FUM A1766 8 HET MN A1767 1 HET MN A1768 1 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM FUM FUMARIC ACID HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 MN 4(MN 2+) FORMUL 5 EPE C8 H18 N2 O4 S FORMUL 6 EDO 8(C2 H6 O2) FORMUL 14 FUM C4 H4 O4 FORMUL 17 HOH *75(H2 O) HELIX 1 1 SER A 38 ALA A 43 1 6 HELIX 2 2 ASP A 44 GLU A 57 1 14 HELIX 3 3 LEU A 379 ASN A 395 1 17 HELIX 4 4 PRO A 402 THR A 416 1 15 HELIX 5 5 SER A 448 GLU A 453 1 6 HELIX 6 6 GLU A 501 SER A 505 5 5 HELIX 7 7 PRO A 523 TYR A 525 5 3 HELIX 8 8 ALA A 526 ALA A 538 1 13 HELIX 9 9 PRO A 539 VAL A 543 5 5 HELIX 10 10 ASN A 557 HIS A 564 1 8 HELIX 11 11 TRP A 607 LEU A 621 1 15 HELIX 12 12 SER A 628 SER A 638 1 11 HELIX 13 13 LYS A 639 LEU A 643 5 5 HELIX 14 14 ASP A 644 LEU A 672 1 29 HELIX 15 15 ASP A 681 LEU A 685 5 5 HELIX 16 16 PRO A 686 ARG A 690 5 5 HELIX 17 17 HIS A 718 LEU A 722 5 5 HELIX 18 18 PRO A 726 TYR A 728 5 3 HELIX 19 19 THR A 737 GLU A 753 1 17 SHEET 1 AA 8 VAL A 34 PHE A 35 0 SHEET 2 AA 8 ILE A 61 VAL A 64 1 O LYS A 63 N PHE A 35 SHEET 3 AA 8 PHE A 578 THR A 581 -1 O PHE A 578 N VAL A 64 SHEET 4 AA 8 TYR A 506 GLY A 514 -1 O SER A 507 N THR A 581 SHEET 5 AA 8 ASN A 595 PHE A 602 -1 O PHE A 596 N HIS A 512 SHEET 6 AA 8 TRP A 486 GLY A 490 -1 O TRP A 486 N ALA A 599 SHEET 7 AA 8 THR A 422 ILE A 429 -1 O GLY A 426 N VAL A 489 SHEET 8 AA 8 ARG A 86 ARG A 89 -1 O ARG A 86 N TYR A 425 SHEET 1 AB 2 HIS A 82 PHE A 83 0 SHEET 2 AB 2 TYR A 377 THR A 378 -1 O TYR A 377 N PHE A 83 SHEET 1 AC 2 GLN A 96 THR A 97 0 SHEET 2 AC 2 LEU A 552 VAL A 553 -1 O VAL A 553 N GLN A 96 SHEET 1 AD 4 SER A 495 HIS A 499 0 SHEET 2 AD 4 HIS A 587 ASN A 591 -1 O HIS A 587 N HIS A 499 SHEET 3 AD 4 LYS A 517 GLY A 521 -1 O THR A 518 N PHE A 590 SHEET 4 AD 4 TYR A 569 GLN A 573 -1 O TYR A 569 N GLY A 521 SHEET 1 AE 3 ASP A 676 ARG A 679 0 SHEET 2 AE 3 TYR A 730 TYR A 734 1 O TYR A 730 N ASP A 676 SHEET 3 AE 3 SER A 702 CYS A 706 -1 O ALA A 703 N ARG A 733 SSBOND 1 CYS A 708 CYS A 725 1555 1555 2.03 LINK OD1 ASN A 91 MN MN A1755 1555 1555 2.56 LINK O THR A 416 MN MN A1755 1555 1555 2.64 LINK NE2 HIS A 499 MN MN A1756 1555 1555 2.12 LINK OE2 GLU A 501 MN MN A1756 1555 1555 2.09 LINK NE2 HIS A 587 MN MN A1756 1555 1555 2.19 LINK SG CYS A 692 ZN ZN A1754 1555 1555 2.16 LINK SG CYS A 695 ZN ZN A1754 1555 1555 2.38 LINK SG CYS A 715 ZN ZN A1754 1555 1555 2.24 LINK ND1 HIS A 718 ZN ZN A1754 1555 1555 2.10 LINK MN MN A1755 O HOH A2015 1555 1555 2.70 LINK MN MN A1756 O8 FUM A1766 1555 1555 2.08 LINK MN MN A1756 O HOH A2034 1555 1555 1.87 LINK MN MN A1756 O HOH A2039 1555 1555 2.18 SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718 SITE 1 AC2 6 LEU A 90 ASN A 91 LEU A 413 THR A 416 SITE 2 AC2 6 GLU A 419 HOH A2015 SITE 1 AC3 6 HIS A 499 GLU A 501 HIS A 587 FUM A1766 SITE 2 AC3 6 HOH A2034 HOH A2039 SITE 1 AC4 13 ILE A 500 TRP A 504 LEU A 541 PHE A 542 SITE 2 AC4 13 LEU A 552 VAL A 553 ARG A 584 TYR A 586 SITE 3 AC4 13 HIS A 617 TYR A 618 LEU A 621 ARG A 623 SITE 4 AC4 13 HOH A2031 SITE 1 AC5 4 ARG A 612 ASP A 630 MET A 658 GLU A 662 SITE 1 AC6 2 PRO A 30 VAL A 568 SITE 1 AC7 6 ASP A 688 GLU A 689 ARG A 690 GLN A 691 SITE 2 AC7 6 GLY A 711 LEU A 713 SITE 1 AC8 1 GLY A 524 SITE 1 AC9 4 ARG A 670 VAL A 674 ILE A 675 HOH A2060 SITE 1 BC1 1 HIS A 564 SITE 1 BC2 4 GLU A 631 LYS A 635 GLU A 683 TYR A 736 SITE 1 BC3 12 TYR A 425 TYR A 488 PHE A 496 HIS A 499 SITE 2 BC3 12 ASN A 509 LYS A 517 TRP A 519 HIS A 587 SITE 3 BC3 12 MN A1756 HOH A2033 HOH A2034 HOH A2039 SITE 1 BC4 2 HIS A 718 HOH A2049 CRYST1 141.680 141.680 153.000 90.00 90.00 120.00 P 65 2 2 12 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 0.007058 0.004075 0.000000 0.00000 SCALE2 0.000000 0.008150 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006536 0.00000