HEADER OXIDOREDUCTASE 19-SEP-17 6EIY
TITLE CRYSTAL STRUCTURE OF KDM5B IN COMPLEX WITH KDOPZ000034A.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B,LYSINE-SPECIFIC DEMETHYLASE
COMPND 3 5B;
COMPND 4 CHAIN: A;
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,CANCER/TESTIS ANTIGEN 31,CT31,
COMPND 8 HISTONE DEMETHYLASE JARID1B,JUMONJI/ARID DOMAIN-CONTAINING PROTEIN
COMPND 9 1B,PLU-1,RETINOBLASTOMA-BINDING PROTEIN 2 HOMOLOG 1,RBP2-H1;
COMPND 10 EC: 1.14.11.-,1.14.11.-;
COMPND 11 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: KDM5B, JARID1B, PLU1, RBBP2H1;
SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108;
SOURCE 8 EXPRESSION_SYSTEM_CELL: SF9;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUSE;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE
KEYWDS KDM5B LYSINE SPECIFIC DEMETHYLASE, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR V.SRIKANNATHASAN,J.A.NEWMAN,A.SZYKOWSKA,M.WRIGHT,G.F.RUDA,
AUTHOR 2 S.A.VAZQUEZ-RODRIGUEZ,K.KUPINSKA,C.STRAIN-DAMERELL,N.A.BURGESS-
AUTHOR 3 BROWN,C.H.ARROWSMITH,A.EDWARDS,C.BOUNTRA,U.OPPERMANN,K.HUBER,F.VON
AUTHOR 4 DELFT
REVDAT 2 17-JAN-24 6EIY 1 LINK
REVDAT 1 02-MAY-18 6EIY 0
JRNL AUTH V.SRIKANNATHASAN
JRNL TITL CRYSTAL STRUCTURE OF KDM5B IN COMPLEX WITH KDOPZ000034A.
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 2.15 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.98
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 49896
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.188
REMARK 3 R VALUE (WORKING SET) : 0.186
REMARK 3 FREE R VALUE : 0.215
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010
REMARK 3 FREE R VALUE TEST SET COUNT : 2501
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.570
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.67
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 : NULL NULL
REMARK 3 ANGLE : NULL NULL
REMARK 3 CHIRALITY : NULL NULL
REMARK 3 PLANARITY : NULL NULL
REMARK 3 DIHEDRAL : NULL NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ALL
REMARK 3 ORIGIN FOR THE GROUP (A): 76.6588 66.4016 11.7505
REMARK 3 T TENSOR
REMARK 3 T11: 0.2994 T22: 0.4992
REMARK 3 T33: 0.3104 T12: -0.0341
REMARK 3 T13: 0.0478 T23: -0.0210
REMARK 3 L TENSOR
REMARK 3 L11: 2.5233 L22: 0.4517
REMARK 3 L33: -0.3563 L12: 0.0741
REMARK 3 L13: 0.2630 L23: 0.0160
REMARK 3 S TENSOR
REMARK 3 S11: 0.0113 S12: -0.0265 S13: 0.1557
REMARK 3 S21: -0.0337 S22: 0.0165 S23: -0.0186
REMARK 3 S31: -0.0051 S32: 0.0177 S33: -0.0303
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 6EIY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-SEP-17.
REMARK 100 THE DEPOSITION ID IS D_1200006686.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-MAR-17
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I04
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950
REMARK 200 MONOCHROMATOR : M
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2
REMARK 200 DATA SCALING SOFTWARE : XIA2
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49958
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150
REMARK 200 RESOLUTION RANGE LOW (A) : 51.983
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 19.60
REMARK 200 R MERGE (I) : 0.11600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 19.00
REMARK 200 R MERGE FOR SHELL (I) : 2.52400
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 5A1F
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 70.63
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.19
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 0.8M POTTASSIUM
REMARK 280 PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC, VAPOR
REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K
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 101.44667
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 50.72333
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 76.08500
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 25.36167
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 126.80833
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 101.44667
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 50.72333
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 25.36167
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 76.08500
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 126.80833
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1630 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 20070 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 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 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 GLY A 370
REMARK 465 GLY A 371
REMARK 465 GLY A 372
REMARK 465 GLY A 373
REMARK 465 LYS A 444
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 40 CG CD OE1 OE2
REMARK 470 LYS A 51 CD CE NZ
REMARK 470 LYS A 100 CG CD CE NZ
REMARK 470 LYS A 408 CE NZ
REMARK 470 LYS A 432 CG CD CE NZ
REMARK 470 GLU A 433 CG CD OE1 OE2
REMARK 470 LYS A 446 NZ
REMARK 470 ASP A 478 CG OD1 OD2
REMARK 470 LYS A 483 CD CE NZ
REMARK 470 LYS A 535 CD CE NZ
REMARK 470 LYS A 536 CD CE NZ
REMARK 470 GLU A 540 CG CD OE1 OE2
REMARK 470 SER A 544 OG
REMARK 470 GLN A 545 CG CD OE1 NE2
REMARK 470 ASP A 547 CG OD1 OD2
REMARK 470 LEU A 548 CG CD1 CD2
REMARK 470 LEU A 549 CG CD1 CD2
REMARK 470 GLN A 551 CG CD OE1 NE2
REMARK 470 LEU A 620 CD1 CD2
REMARK 470 LYS A 639 NZ
REMARK 470 LYS A 653 CE NZ
REMARK 470 LYS A 671 NZ
REMARK 470 LYS A 694 NZ
REMARK 470 LYS A 709 CE NZ
REMARK 470 LYS A 720 CG CD CE NZ
REMARK 470 GLU A 753 CD OE1 OE2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 1064 O HOH A 1064 9765 2.08
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 LEU A 93 -0.48 74.91
REMARK 500 ARG A 375 163.89 -45.23
REMARK 500 PHE A 434 95.94 -163.19
REMARK 500 ILE A 479 64.78 -118.40
REMARK 500 PHE A 493 -10.34 79.98
REMARK 500 PHE A 700 -53.88 -150.62
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 A 802 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN A 91 OD1
REMARK 620 2 LEU A 413 O 150.8
REMARK 620 3 THR A 416 O 119.9 79.5
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 809 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 499 NE2
REMARK 620 2 GLU A 501 OE1 96.8
REMARK 620 3 HIS A 587 NE2 87.5 84.7
REMARK 620 4 B6W A 810 N4 92.2 169.2 101.6
REMARK 620 5 HOH A 965 O 179.1 84.0 92.4 86.9
REMARK 620 6 HOH A 995 O 91.6 91.5 175.9 82.4 88.5
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 801 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 692 SG
REMARK 620 2 CYS A 695 SG 106.9
REMARK 620 3 CYS A 715 SG 119.6 110.6
REMARK 620 4 HIS A 718 ND1 111.4 105.6 102.0
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 801
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 802
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 803
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 804
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 805
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 806
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 807
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 808
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 809
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue B6W A 810
DBREF 6EIY A 26 100 UNP Q9UGL1 KDM5B_HUMAN 26 100
DBREF 6EIY A 374 754 UNP Q9UGL1 KDM5B_HUMAN 374 754
SEQADV 6EIY MET A 25 UNP Q9UGL1 INITIATING METHIONINE
SEQADV 6EIY GLY A 370 UNP Q9UGL1 LINKER
SEQADV 6EIY GLY A 371 UNP Q9UGL1 LINKER
SEQADV 6EIY GLY A 372 UNP Q9UGL1 LINKER
SEQADV 6EIY GLY A 373 UNP Q9UGL1 LINKER
SEQRES 1 A 461 MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU PRO
SEQRES 2 A 461 SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE HIS
SEQRES 3 A 461 LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS LYS
SEQRES 4 A 461 VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA CYS
SEQRES 5 A 461 ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN ARG
SEQRES 6 A 461 LEU ASN GLU LEU GLU ALA GLN THR ARG VAL LYS GLY GLY
SEQRES 7 A 461 GLY GLY ALA ARG ASP TYR THR LEU ARG THR PHE GLY GLU
SEQRES 8 A 461 MET ALA ASP ALA PHE LYS SER ASP TYR PHE ASN MET PRO
SEQRES 9 A 461 VAL HIS MET VAL PRO THR GLU LEU VAL GLU LYS GLU PHE
SEQRES 10 A 461 TRP ARG LEU VAL SER THR ILE GLU GLU ASP VAL THR VAL
SEQRES 11 A 461 GLU TYR GLY ALA ASP ILE ALA SER LYS GLU PHE GLY SER
SEQRES 12 A 461 GLY PHE PRO VAL ARG ASP GLY LYS ILE LYS LEU SER PRO
SEQRES 13 A 461 GLU GLU GLU GLU TYR LEU ASP SER GLY TRP ASN LEU ASN
SEQRES 14 A 461 ASN MET PRO VAL MET GLU GLN SER VAL LEU ALA HIS ILE
SEQRES 15 A 461 THR ALA ASP ILE CYS GLY MET LYS LEU PRO TRP LEU TYR
SEQRES 16 A 461 VAL GLY MET CYS PHE SER SER PHE CYS TRP HIS ILE GLU
SEQRES 17 A 461 ASP HIS TRP SER TYR SER ILE ASN TYR LEU HIS TRP GLY
SEQRES 18 A 461 GLU PRO LYS THR TRP TYR GLY VAL PRO GLY TYR ALA ALA
SEQRES 19 A 461 GLU GLN LEU GLU ASN VAL MET LYS LYS LEU ALA PRO GLU
SEQRES 20 A 461 LEU PHE VAL SER GLN PRO ASP LEU LEU HIS GLN LEU VAL
SEQRES 21 A 461 THR ILE MET ASN PRO ASN THR LEU MET THR HIS GLU VAL
SEQRES 22 A 461 PRO VAL TYR ARG THR ASN GLN CYS ALA GLY GLU PHE VAL
SEQRES 23 A 461 ILE THR PHE PRO ARG ALA TYR HIS SER GLY PHE ASN GLN
SEQRES 24 A 461 GLY PHE ASN PHE ALA GLU ALA VAL ASN PHE CYS THR VAL
SEQRES 25 A 461 ASP TRP LEU PRO LEU GLY ARG GLN CYS VAL GLU HIS TYR
SEQRES 26 A 461 ARG LEU LEU HIS ARG TYR CYS VAL PHE SER HIS ASP GLU
SEQRES 27 A 461 MET ILE CYS LYS MET ALA SER LYS ALA ASP VAL LEU ASP
SEQRES 28 A 461 VAL VAL VAL ALA SER THR VAL GLN LYS ASP MET ALA ILE
SEQRES 29 A 461 MET ILE GLU ASP GLU LYS ALA LEU ARG GLU THR VAL ARG
SEQRES 30 A 461 LYS LEU GLY VAL ILE ASP SER GLU ARG MET ASP PHE GLU
SEQRES 31 A 461 LEU LEU PRO ASP ASP GLU ARG GLN CYS VAL LYS CYS LYS
SEQRES 32 A 461 THR THR CYS PHE MET SER ALA ILE SER CYS SER CYS LYS
SEQRES 33 A 461 PRO GLY LEU LEU VAL CYS LEU HIS HIS VAL LYS GLU LEU
SEQRES 34 A 461 CYS SER CYS PRO PRO TYR LYS TYR LYS LEU ARG TYR ARG
SEQRES 35 A 461 TYR THR LEU ASP ASP LEU TYR PRO MET MET ASN ALA LEU
SEQRES 36 A 461 LYS LEU ARG ALA GLU SER
HET ZN A 801 1
HET MN A 802 1
HET EDO A 803 4
HET EDO A 804 4
HET EDO A 805 4
HET DMS A 806 4
HET DMS A 807 4
HET DMS A 808 4
HET MN A 809 1
HET B6W A 810 27
HETNAM ZN ZINC ION
HETNAM MN MANGANESE (II) ION
HETNAM EDO 1,2-ETHANEDIOL
HETNAM DMS DIMETHYL SULFOXIDE
HETNAM B6W 2-CHLORANYL-~{N}-[2-[4-(3-CYANO-7-OXIDANYLIDENE-6-
HETNAM 2 B6W PROPAN-2-YL-4~{H}-PYRAZOLO[1,5-A]PYRIMIDIN-5-YL)
HETNAM 3 B6W PYRAZOL-1-YL]ETHYL]ETHANAMIDE
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 ZN ZN 2+
FORMUL 3 MN 2(MN 2+)
FORMUL 4 EDO 3(C2 H6 O2)
FORMUL 7 DMS 3(C2 H6 O S)
FORMUL 11 B6W C17 H18 CL N7 O2
FORMUL 12 HOH *185(H2 O)
HELIX 1 AA1 SER A 38 ALA A 43 1 6
HELIX 2 AA2 ASP A 44 GLU A 57 1 14
HELIX 3 AA3 LEU A 379 ASN A 395 1 17
HELIX 4 AA4 PRO A 397 VAL A 401 5 5
HELIX 5 AA5 PRO A 402 THR A 416 1 15
HELIX 6 AA6 SER A 448 TYR A 454 1 7
HELIX 7 AA7 ASN A 460 MET A 467 5 8
HELIX 8 AA8 SER A 470 ILE A 475 5 6
HELIX 9 AA9 ILE A 479 LEU A 484 1 6
HELIX 10 AB1 GLU A 501 SER A 505 5 5
HELIX 11 AB2 PRO A 523 TYR A 525 5 3
HELIX 12 AB3 ALA A 526 ALA A 538 1 13
HELIX 13 AB4 PRO A 539 VAL A 543 5 5
HELIX 14 AB5 ASP A 547 GLN A 551 5 5
HELIX 15 AB6 ASN A 557 HIS A 564 1 8
HELIX 16 AB7 THR A 604 ASP A 606 5 3
HELIX 17 AB8 TRP A 607 HIS A 622 1 16
HELIX 18 AB9 SER A 628 LYS A 639 1 12
HELIX 19 AC1 ALA A 640 LEU A 643 5 4
HELIX 20 AC2 ASP A 644 LEU A 672 1 29
HELIX 21 AC3 ASP A 681 LEU A 685 5 5
HELIX 22 AC4 PRO A 686 ARG A 690 5 5
HELIX 23 AC5 CYS A 715 LEU A 722 5 8
HELIX 24 AC6 PRO A 726 TYR A 728 5 3
HELIX 25 AC7 THR A 737 SER A 754 1 18
SHEET 1 AA1 8 VAL A 34 PHE A 35 0
SHEET 2 AA1 8 ILE A 61 VAL A 64 1 O LYS A 63 N PHE A 35
SHEET 3 AA1 8 PHE A 578 THR A 581 -1 O PHE A 578 N VAL A 64
SHEET 4 AA1 8 TYR A 506 GLY A 514 -1 N SER A 507 O THR A 581
SHEET 5 AA1 8 ASN A 595 PHE A 602 -1 O GLU A 598 N TYR A 510
SHEET 6 AA1 8 TRP A 486 GLY A 490 -1 N TRP A 486 O ALA A 599
SHEET 7 AA1 8 THR A 422 ILE A 429 -1 N ASP A 428 O LEU A 487
SHEET 8 AA1 8 ARG A 86 ARG A 89 -1 N GLN A 88 O VAL A 423
SHEET 1 AA2 2 HIS A 82 PHE A 83 0
SHEET 2 AA2 2 TYR A 377 THR A 378 -1 O TYR A 377 N PHE A 83
SHEET 1 AA3 4 SER A 495 HIS A 499 0
SHEET 2 AA3 4 HIS A 587 ASN A 591 -1 O GLY A 589 N PHE A 496
SHEET 3 AA3 4 LYS A 517 GLY A 521 -1 N THR A 518 O PHE A 590
SHEET 4 AA3 4 TYR A 569 GLN A 573 -1 O GLN A 573 N LYS A 517
SHEET 1 AA4 3 ASP A 676 ARG A 679 0
SHEET 2 AA4 3 TYR A 730 TYR A 734 1 O LEU A 732 N GLU A 678
SHEET 3 AA4 3 SER A 702 CYS A 706 -1 N ALA A 703 O ARG A 733
SSBOND 1 CYS A 706 CYS A 723 1555 1555 2.11
SSBOND 2 CYS A 708 CYS A 725 1555 1555 2.02
LINK OD1 ASN A 91 MN MN A 802 1555 1555 2.64
LINK O LEU A 413 MN MN A 802 1555 1555 2.71
LINK O THR A 416 MN MN A 802 1555 1555 2.76
LINK NE2 HIS A 499 MN MN A 809 1555 1555 2.10
LINK OE1 GLU A 501 MN MN A 809 1555 1555 1.97
LINK NE2 HIS A 587 MN MN A 809 1555 1555 2.19
LINK SG CYS A 692 ZN ZN A 801 1555 1555 2.29
LINK SG CYS A 695 ZN ZN A 801 1555 1555 2.35
LINK SG CYS A 715 ZN ZN A 801 1555 1555 2.28
LINK ND1 HIS A 718 ZN ZN A 801 1555 1555 2.09
LINK MN MN A 809 N4 B6W A 810 1555 1555 2.10
LINK MN MN A 809 O HOH A 965 1555 1555 2.13
LINK MN MN A 809 O HOH A 995 1555 1555 2.19
SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718
SITE 1 AC2 5 LEU A 90 ASN A 91 LEU A 413 THR A 416
SITE 2 AC2 5 GLU A 419
SITE 1 AC3 6 ASP A 630 CYS A 699 PHE A 700 MET A 701
SITE 2 AC3 6 SER A 702 HOH A 936
SITE 1 AC4 3 GLY A 524 TYR A 525 ARG A 584
SITE 1 AC5 6 PHE A 83 GLY A 426 ALA A 427 ASP A 428
SITE 2 AC5 6 LEU A 487 VAL A 489
SITE 1 AC6 7 ILE A 500 TRP A 504 HIS A 617 TYR A 618
SITE 2 AC6 7 LEU A 621 ARG A 623 HOH A 983
SITE 1 AC7 7 TRP A 486 TYR A 488 SER A 507 ALA A 599
SITE 2 AC7 7 VAL A 600 ASN A 601 HOH A 995
SITE 1 AC8 3 HIS A 622 HIS A 718 HOH A 998
SITE 1 AC9 6 HIS A 499 GLU A 501 HIS A 587 B6W A 810
SITE 2 AC9 6 HOH A 965 HOH A 995
SITE 1 AD1 18 GLN A 88 GLN A 96 THR A 97 TYR A 425
SITE 2 AD1 18 GLY A 426 TYR A 488 SER A 495 PHE A 496
SITE 3 AD1 18 CYS A 497 HIS A 499 ASN A 509 LYS A 517
SITE 4 AD1 18 HIS A 587 ASN A 591 MN A 809 HOH A 965
SITE 5 AD1 18 HOH A 995 HOH A1037
CRYST1 142.380 142.380 152.170 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 0.007023 0.004055 0.000000 0.00000
SCALE2 0.000000 0.008110 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006572 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
