HEADER OXIDOREDUCTASE 19-SEP-17 6EJ0 TITLE CRYSTAL STRUCTURE OF KDM5B IN COMPLEX WITH KDOPZ000049A. CAVEAT 6EJ0 B7K A 811 HAS WRONG CHIRALITY AT ATOM C5 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_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUSE; SOURCE 11 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 1 02-MAY-18 6EJ0 0 JRNL AUTH V.SRIKANNATHASAN JRNL TITL CRYSTAL STRUCTURE OF KDM5B IN COMPLEX WITH KDOPZ000049A. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 56007 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 2869 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 51.8237 - 5.5895 1.00 2921 147 0.1810 0.1993 REMARK 3 2 5.5895 - 4.4373 1.00 2736 157 0.1492 0.1524 REMARK 3 3 4.4373 - 3.8766 1.00 2717 150 0.1492 0.1629 REMARK 3 4 3.8766 - 3.5223 1.00 2686 133 0.1732 0.1496 REMARK 3 5 3.5223 - 3.2699 1.00 2705 129 0.1988 0.2573 REMARK 3 6 3.2699 - 3.0771 1.00 2636 152 0.2083 0.2517 REMARK 3 7 3.0771 - 2.9230 1.00 2660 144 0.2134 0.2443 REMARK 3 8 2.9230 - 2.7958 1.00 2642 143 0.2114 0.2424 REMARK 3 9 2.7958 - 2.6882 1.00 2658 147 0.2153 0.2521 REMARK 3 10 2.6882 - 2.5954 1.00 2583 166 0.2170 0.2461 REMARK 3 11 2.5954 - 2.5143 1.00 2645 144 0.2140 0.2471 REMARK 3 12 2.5143 - 2.4424 1.00 2610 146 0.2163 0.2544 REMARK 3 13 2.4424 - 2.3781 1.00 2653 125 0.2286 0.2663 REMARK 3 14 2.3781 - 2.3201 1.00 2607 157 0.2264 0.2899 REMARK 3 15 2.3201 - 2.2673 1.00 2609 152 0.2384 0.2572 REMARK 3 16 2.2673 - 2.2191 1.00 2614 126 0.2475 0.2819 REMARK 3 17 2.2191 - 2.1747 1.00 2632 118 0.2547 0.3123 REMARK 3 18 2.1747 - 2.1336 1.00 2601 162 0.2632 0.3043 REMARK 3 19 2.1336 - 2.0955 1.00 2620 135 0.2762 0.3264 REMARK 3 20 2.0955 - 2.0600 1.00 2603 136 0.2739 0.2806 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 3794 REMARK 3 ANGLE : 0.979 5166 REMARK 3 CHIRALITY : 0.061 551 REMARK 3 PLANARITY : 0.006 691 REMARK 3 DIHEDRAL : 5.482 3098 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): 76.4595 66.2565 11.6270 REMARK 3 T TENSOR REMARK 3 T11: 0.2559 T22: 0.4181 REMARK 3 T33: 0.2753 T12: -0.0382 REMARK 3 T13: 0.0352 T23: -0.0465 REMARK 3 L TENSOR REMARK 3 L11: 2.2761 L22: 0.3807 REMARK 3 L33: 0.0055 L12: 0.1116 REMARK 3 L13: 0.1813 L23: -0.1275 REMARK 3 S TENSOR REMARK 3 S11: -0.0176 S12: 0.0086 S13: 0.0794 REMARK 3 S21: -0.0186 S22: 0.0262 S23: 0.0399 REMARK 3 S31: 0.0157 S32: 0.0495 S33: -0.0030 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: UNDEFINED SIDE CHAINS REMOVED. RESIDUES REMARK 3 WITHOUT DENSITY DELETED. REMARK 4 REMARK 4 6EJ0 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_1200006689. 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 : 56074 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 REMARK 200 RESOLUTION RANGE LOW (A) : 64.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.80 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.00 REMARK 200 R MERGE FOR SHELL (I) : 2.41600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.17 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 101.16667 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 50.58333 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 75.87500 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 25.29167 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 126.45833 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 101.16667 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 50.58333 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 25.29167 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 75.87500 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 126.45833 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 TOTAL BURIED SURFACE AREA: 1920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 7.0 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 371 REMARK 465 GLY A 372 REMARK 465 GLY A 373 REMARK 465 GLY A 374 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 PHE A 74 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 98 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 375 CG CD NE CZ NH1 NH2 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 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 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 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 1034 O HOH A 1070 2.07 REMARK 500 O HIS A 399 O HOH A 901 2.12 REMARK 500 O MET A 467 O HOH A 902 2.15 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 93.82 -63.24 REMARK 500 LEU A 93 -3.49 70.85 REMARK 500 ASP A 420 71.45 -104.36 REMARK 500 PHE A 434 98.95 -168.10 REMARK 500 ASP A 442 115.38 -165.07 REMARK 500 ALA A 477 108.89 -49.85 REMARK 500 ASP A 478 102.15 -56.22 REMARK 500 CYS A 480 -54.46 67.41 REMARK 500 PHE A 493 -6.58 79.48 REMARK 500 SER A 544 106.60 -57.53 REMARK 500 PHE A 700 -51.97 -148.57 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 150.0 REMARK 620 3 THR A 416 O 123.0 81.8 REMARK 620 4 HOH A 909 O 75.9 102.3 129.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 810 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 499 NE2 REMARK 620 2 GLU A 501 OE2 98.3 REMARK 620 3 HIS A 587 NE2 89.5 84.2 REMARK 620 4 B7K A 811 N2 94.4 166.3 100.9 REMARK 620 5 HOH A 975 O 91.6 90.3 174.5 84.4 REMARK 620 6 HOH A 926 O 178.6 81.1 89.2 86.3 89.7 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 105.5 REMARK 620 3 CYS A 715 SG 121.4 109.8 REMARK 620 4 HIS A 718 ND1 111.9 106.4 101.0 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 DMS 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 DMS A 809 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 810 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B7K A 811 DBREF 6EJ0 A 26 98 UNP Q9UGL1 KDM5B_HUMAN 26 98 DBREF 6EJ0 A 375 754 UNP Q9UGL1 KDM5B_HUMAN 375 754 SEQADV 6EJ0 MET A 25 UNP Q9UGL1 INITIATING METHIONINE SEQADV 6EJ0 GLY A 371 UNP Q9UGL1 LINKER SEQADV 6EJ0 GLY A 372 UNP Q9UGL1 LINKER SEQADV 6EJ0 GLY A 373 UNP Q9UGL1 LINKER SEQADV 6EJ0 GLY A 374 UNP Q9UGL1 LINKER SEQRES 1 A 458 MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU PRO SEQRES 2 A 458 SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE HIS SEQRES 3 A 458 LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS LYS SEQRES 4 A 458 VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA CYS SEQRES 5 A 458 ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN ARG SEQRES 6 A 458 LEU ASN GLU LEU GLU ALA GLN THR ARG GLY GLY GLY GLY SEQRES 7 A 458 ARG ASP TYR THR LEU ARG THR PHE GLY GLU MET ALA ASP SEQRES 8 A 458 ALA PHE LYS SER ASP TYR PHE ASN MET PRO VAL HIS MET SEQRES 9 A 458 VAL PRO THR GLU LEU VAL GLU LYS GLU PHE TRP ARG LEU SEQRES 10 A 458 VAL SER THR ILE GLU GLU ASP VAL THR VAL GLU TYR GLY SEQRES 11 A 458 ALA ASP ILE ALA SER LYS GLU PHE GLY SER GLY PHE PRO SEQRES 12 A 458 VAL ARG ASP GLY LYS ILE LYS LEU SER PRO GLU GLU GLU SEQRES 13 A 458 GLU TYR LEU ASP SER GLY TRP ASN LEU ASN ASN MET PRO SEQRES 14 A 458 VAL MET GLU GLN SER VAL LEU ALA HIS ILE THR ALA ASP SEQRES 15 A 458 ILE CYS GLY MET LYS LEU PRO TRP LEU TYR VAL GLY MET SEQRES 16 A 458 CYS PHE SER SER PHE CYS TRP HIS ILE GLU ASP HIS TRP SEQRES 17 A 458 SER TYR SER ILE ASN TYR LEU HIS TRP GLY GLU PRO LYS SEQRES 18 A 458 THR TRP TYR GLY VAL PRO GLY TYR ALA ALA GLU GLN LEU SEQRES 19 A 458 GLU ASN VAL MET LYS LYS LEU ALA PRO GLU LEU PHE VAL SEQRES 20 A 458 SER GLN PRO ASP LEU LEU HIS GLN LEU VAL THR ILE MET SEQRES 21 A 458 ASN PRO ASN THR LEU MET THR HIS GLU VAL PRO VAL TYR SEQRES 22 A 458 ARG THR ASN GLN CYS ALA GLY GLU PHE VAL ILE THR PHE SEQRES 23 A 458 PRO ARG ALA TYR HIS SER GLY PHE ASN GLN GLY PHE ASN SEQRES 24 A 458 PHE ALA GLU ALA VAL ASN PHE CYS THR VAL ASP TRP LEU SEQRES 25 A 458 PRO LEU GLY ARG GLN CYS VAL GLU HIS TYR ARG LEU LEU SEQRES 26 A 458 HIS ARG TYR CYS VAL PHE SER HIS ASP GLU MET ILE CYS SEQRES 27 A 458 LYS MET ALA SER LYS ALA ASP VAL LEU ASP VAL VAL VAL SEQRES 28 A 458 ALA SER THR VAL GLN LYS ASP MET ALA ILE MET ILE GLU SEQRES 29 A 458 ASP GLU LYS ALA LEU ARG GLU THR VAL ARG LYS LEU GLY SEQRES 30 A 458 VAL ILE ASP SER GLU ARG MET ASP PHE GLU LEU LEU PRO SEQRES 31 A 458 ASP ASP GLU ARG GLN CYS VAL LYS CYS LYS THR THR CYS SEQRES 32 A 458 PHE MET SER ALA ILE SER CYS SER CYS LYS PRO GLY LEU SEQRES 33 A 458 LEU VAL CYS LEU HIS HIS VAL LYS GLU LEU CYS SER CYS SEQRES 34 A 458 PRO PRO TYR LYS TYR LYS LEU ARG TYR ARG TYR THR LEU SEQRES 35 A 458 ASP ASP LEU TYR PRO MET MET ASN ALA LEU LYS LEU ARG SEQRES 36 A 458 ALA GLU SER HET ZN A 801 1 HET MN A 802 1 HET EDO A 803 4 HET EDO A 804 4 HET DMS A 805 4 HET DMS A 806 4 HET DMS A 807 4 HET DMS A 808 4 HET DMS A 809 4 HET MN A 810 1 HET B7K A 811 30 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETNAM B7K 7-OXIDANYLIDENE-6-PROPAN-2-YL-5-[1-(1-PROP-2- HETNAM 2 B7K ENOYLPIPERIDIN-4-YL)PYRAZOL-4-YL]-6~{H}-PYRAZOLO[1,5- HETNAM 3 B7K A]PYRIMIDINE-3-CARBONITRILE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 MN 2(MN 2+) FORMUL 4 EDO 2(C2 H6 O2) FORMUL 6 DMS 5(C2 H6 O S) FORMUL 12 B7K C21 H23 N7 O2 FORMUL 13 HOH *177(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 463 MET A 467 5 5 HELIX 8 AA8 GLU A 501 SER A 505 5 5 HELIX 9 AA9 PRO A 523 TYR A 525 5 3 HELIX 10 AB1 ALA A 526 ALA A 538 1 13 HELIX 11 AB2 PRO A 539 VAL A 543 5 5 HELIX 12 AB3 ASN A 557 HIS A 564 1 8 HELIX 13 AB4 THR A 604 ASP A 606 5 3 HELIX 14 AB5 TRP A 607 HIS A 622 1 16 HELIX 15 AB6 SER A 628 LYS A 639 1 12 HELIX 16 AB7 ALA A 640 LEU A 643 5 4 HELIX 17 AB8 ASP A 644 LEU A 672 1 29 HELIX 18 AB9 ASP A 681 LEU A 685 5 5 HELIX 19 AC1 PRO A 686 ARG A 690 5 5 HELIX 20 AC2 HIS A 718 LEU A 722 5 5 HELIX 21 AC3 PRO A 726 TYR A 728 5 3 HELIX 22 AC4 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 ASN A 509 O VAL A 579 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 TYR A 488 O ALA A 597 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 ARG A 86 O TYR A 425 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 2 GLN A 96 THR A 97 0 SHEET 2 AA3 2 LEU A 552 VAL A 553 -1 O VAL A 553 N GLN A 96 SHEET 1 AA4 4 SER A 495 HIS A 499 0 SHEET 2 AA4 4 HIS A 587 ASN A 591 -1 O HIS A 587 N HIS A 499 SHEET 3 AA4 4 LYS A 517 GLY A 521 -1 N THR A 518 O PHE A 590 SHEET 4 AA4 4 TYR A 569 GLN A 573 -1 O GLN A 573 N LYS A 517 SHEET 1 AA5 3 SER A 677 ARG A 679 0 SHEET 2 AA5 3 TYR A 730 TYR A 734 1 O LEU A 732 N GLU A 678 SHEET 3 AA5 3 SER A 702 CYS A 706 -1 N ALA A 703 O ARG A 733 SSBOND 1 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 2.74 LINK O THR A 416 MN MN A 802 1555 1555 2.63 LINK NE2 HIS A 499 MN MN A 810 1555 1555 2.03 LINK OE2 GLU A 501 MN MN A 810 1555 1555 2.05 LINK NE2 HIS A 587 MN MN A 810 1555 1555 2.15 LINK SG CYS A 692 ZN ZN A 801 1555 1555 2.30 LINK SG CYS A 695 ZN ZN A 801 1555 1555 2.34 LINK SG CYS A 715 ZN ZN A 801 1555 1555 2.25 LINK ND1 HIS A 718 ZN ZN A 801 1555 1555 2.10 LINK MN MN A 802 O HOH A 909 1555 1555 2.40 LINK MN MN A 810 N2 B7K A 811 1555 1555 2.09 LINK MN MN A 810 O HOH A 975 1555 1555 2.15 LINK MN MN A 810 O HOH A 926 1555 1555 1.90 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 A 909 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 938 SITE 1 AC4 3 GLY A 524 TYR A 525 ARG A 584 SITE 1 AC5 7 ILE A 500 TRP A 504 GLU A 531 ARG A 584 SITE 2 AC5 7 HIS A 617 TYR A 618 ARG A 623 SITE 1 AC6 8 TRP A 486 TYR A 488 GLU A 501 SER A 507 SITE 2 AC6 8 ALA A 599 VAL A 600 ASN A 601 HOH A 975 SITE 1 AC7 7 PHE A 83 GLY A 426 ALA A 427 ASP A 428 SITE 2 AC7 7 PHE A 434 LEU A 487 HOH A1017 SITE 1 AC8 4 GLU A 631 LYS A 635 GLU A 683 TYR A 736 SITE 1 AC9 3 HIS A 622 HIS A 718 HOH A1031 SITE 1 AD1 6 HIS A 499 GLU A 501 HIS A 587 B7K A 811 SITE 2 AD1 6 HOH A 926 HOH A 975 SITE 1 AD2 17 ARG A 86 ARG A 98 TYR A 425 GLY A 426 SITE 2 AD2 17 TRP A 486 TYR A 488 PHE A 496 HIS A 499 SITE 3 AD2 17 ASN A 509 LYS A 517 HIS A 587 ASN A 591 SITE 4 AD2 17 MN A 810 HOH A 910 HOH A 926 HOH A 975 SITE 5 AD2 17 HOH A1009 CRYST1 141.820 141.820 151.750 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 0.007051 0.004071 0.000000 0.00000 SCALE2 0.000000 0.008142 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006590 0.00000