HEADER OXIDOREDUCTASE 23-JUL-18 6H51 TITLE CRYSTAL STRUCTURE OF HUMAN KDM5B IN COMPLEX WITH COMPOUND 34F 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_LINE: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS HISTONE DEMETHYLASE, INHIBITOR, TRANSCRIPTION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.V.LE BIHAN,S.VELUPILLAI,R.L.M.VAN MONTFORT REVDAT 2 17-JAN-24 6H51 1 REMARK REVDAT 1 12-JUN-19 6H51 0 JRNL AUTH Y.V.LE BIHAN,R.M.LANIGAN,B.ATRASH,M.G.MCLAUGHLIN, JRNL AUTH 2 S.VELUPILLAI,A.G.MALCOLM,K.S.ENGLAND,G.F.RUDA,N.Y.MOK, JRNL AUTH 3 A.TUMBER,K.TOMLIN,H.SAVILLE,E.SHEHU,C.MCANDREW,L.CARMICHAEL, JRNL AUTH 4 J.M.BENNETT,F.JEGANATHAN,P.EVE,A.DONOVAN,A.HAYES,F.WOOD, JRNL AUTH 5 F.I.RAYNAUD,O.FEDOROV,P.E.BRENNAN,R.BURKE, JRNL AUTH 6 R.L.M.VAN MONTFORT,O.W.ROSSANESE,J.BLAGG,V.BAVETSIAS JRNL TITL C8-SUBSTITUTED PYRIDO[3,4-D]PYRIMIDIN-4(3H)-ONES: STUDIES JRNL TITL 2 TOWARDS THE IDENTIFICATION OF POTENT, CELL PENETRANT JUMONJI JRNL TITL 3 C DOMAIN CONTAINING HISTONE LYSINE DEMETHYLASE 4 SUBFAMILY JRNL TITL 4 (KDM4) INHIBITORS, COMPOUND PROFILING IN CELL-BASED TARGET JRNL TITL 5 ENGAGEMENT ASSAYS. JRNL REF EUR.J.MED.CHEM. V. 177 316 2019 JRNL REFN ISSN 0223-5234 JRNL PMID 31158747 JRNL DOI 10.1016/J.EJMECH.2019.05.041 REMARK 2 REMARK 2 RESOLUTION. 2.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 45821 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 2231 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.21 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.27 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3322 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2323 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3172 REMARK 3 BIN R VALUE (WORKING SET) : 0.2311 REMARK 3 BIN FREE R VALUE : 0.2593 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.52 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 150 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3569 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 282 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.82150 REMARK 3 B22 (A**2) : -0.82150 REMARK 3 B33 (A**2) : 1.64300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.260 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.155 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.132 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.146 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.128 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3806 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 5182 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1247 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 79 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 576 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3806 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 2 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 476 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 13 ; 1.000 ; HARMONIC REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 4432 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.05 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.46 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.47 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|24 - 607} REMARK 3 ORIGIN FOR THE GROUP (A): 87.4825 67.3939 15.4295 REMARK 3 T TENSOR REMARK 3 T11: -0.2146 T22: 0.0307 REMARK 3 T33: -0.1063 T12: -0.0746 REMARK 3 T13: 0.0220 T23: -0.0487 REMARK 3 L TENSOR REMARK 3 L11: 1.8159 L22: 1.1175 REMARK 3 L33: 2.8135 L12: -0.1298 REMARK 3 L13: 0.4067 L23: -0.1955 REMARK 3 S TENSOR REMARK 3 S11: -0.0183 S12: -0.1471 S13: 0.0350 REMARK 3 S21: 0.0066 S22: -0.0069 S23: 0.0266 REMARK 3 S31: 0.2322 S32: -0.1195 S33: 0.0253 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|608 - 754} REMARK 3 ORIGIN FOR THE GROUP (A): 55.4732 63.9107 5.1917 REMARK 3 T TENSOR REMARK 3 T11: -0.1935 T22: 0.0160 REMARK 3 T33: 0.0076 T12: -0.0146 REMARK 3 T13: -0.0253 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 2.0464 L22: 2.0464 REMARK 3 L33: 2.4848 L12: 0.0896 REMARK 3 L13: 0.1064 L23: 0.6353 REMARK 3 S TENSOR REMARK 3 S11: -0.1507 S12: 0.1483 S13: 0.1699 REMARK 3 S21: -0.0903 S22: 0.2385 S23: 0.1298 REMARK 3 S31: -0.0464 S32: 0.2428 S33: -0.0878 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6H51 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1200009514. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-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 : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45895 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 REMARK 200 RESOLUTION RANGE LOW (A) : 51.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 17.10 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.90 REMARK 200 R MERGE FOR SHELL (I) : 1.49100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: 5A1F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 NL OF PROTEIN IS MIXED WITH 200 NL REMARK 280 OF CRYSTALLISATION SOLUTION CONTAINING 1.6 M NA/K PHOSPHATE, 0.1 REMARK 280 M HEPES PH 7.5, AND WITH 20 NL OF SEEDS OBTAINED IN THE SAME REMARK 280 CONDITIONS. INHIBITOR IS SOAKED IN CRYSTALS BY ADDITION DIRECTLY REMARK 280 TO THE DROPS OF DMSO DISSOLVED COMPOUND, VAPOR DIFFUSION, REMARK 280 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 101.60667 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 50.80333 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 76.20500 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 25.40167 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 127.00833 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 101.60667 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 50.80333 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 25.40167 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 76.20500 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 127.00833 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: 2590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 8.0 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 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 A1105 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 368 REMARK 465 LEU A 369 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 465 GLN A 545 REMARK 465 PRO A 546 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 465 ASN A 771 REMARK 465 LYS A 772 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 SER A 24 N CB OG REMARK 470 GLU A 40 CG CD OE1 OE2 REMARK 470 LYS A 51 CE NZ REMARK 470 LEU A 81 CD1 CD2 REMARK 470 ARG A 98 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 99 CA C O CB CG1 CG2 REMARK 470 ARG A 375 CZ NH1 NH2 REMARK 470 LYS A 408 CE NZ REMARK 470 ILE A 417 CD1 REMARK 470 GLU A 418 CG CD OE1 OE2 REMARK 470 ASP A 420 OD1 OD2 REMARK 470 ASP A 428 CG OD1 OD2 REMARK 470 ILE A 429 CG1 CD1 REMARK 470 LYS A 432 CG CD CE NZ REMARK 470 GLU A 433 CG CD OE1 OE2 REMARK 470 ILE A 445 CD1 REMARK 470 LYS A 446 CE NZ REMARK 470 ILE A 475 CD1 REMARK 470 ASP A 478 CG OD1 OD2 REMARK 470 LYS A 483 CG CD CE NZ REMARK 470 GLU A 528 CD OE1 OE2 REMARK 470 LYS A 535 CD CE NZ REMARK 470 LYS A 536 CE NZ REMARK 470 GLU A 540 CG CD OE1 OE2 REMARK 470 VAL A 543 CG1 REMARK 470 SER A 544 CA C O CB OG 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 GLU A 565 CG CD OE1 OE2 REMARK 470 LYS A 639 NZ REMARK 470 LYS A 653 CE NZ REMARK 470 LYS A 663 NZ REMARK 470 LYS A 671 NZ REMARK 470 LYS A 694 NZ REMARK 470 LYS A 709 NZ REMARK 470 LYS A 720 CD CE NZ REMARK 470 LYS A 729 NZ REMARK 470 LYS A 731 NZ REMARK 470 LYS A 749 CE NZ REMARK 470 GLU A 753 OE1 OE2 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 ASP A 420 58.46 -117.93 REMARK 500 CYS A 480 -39.20 -34.20 REMARK 500 PHE A 493 -6.52 75.40 REMARK 500 PHE A 700 -58.40 -137.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 FQK A 816 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 803 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 413 O REMARK 620 2 LEU A 413 O 4.0 REMARK 620 3 THR A 416 O 87.3 91.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 804 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 499 NE2 REMARK 620 2 GLU A 501 OE2 95.3 REMARK 620 3 HIS A 587 NE2 83.9 80.9 REMARK 620 4 FQK A 816 N4 81.6 100.7 165.5 REMARK 620 5 FQK A 816 N 98.0 166.7 100.3 81.5 REMARK 620 6 FQK A 816 N3 80.3 128.2 147.8 27.6 54.9 REMARK 620 7 HOH A 950 O 174.8 83.7 90.9 103.6 83.0 104.3 REMARK 620 N 1 2 3 4 5 6 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 107.0 REMARK 620 3 CYS A 715 SG 117.4 110.6 REMARK 620 4 HIS A 718 ND1 110.9 109.7 101.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 706 SG REMARK 620 2 CYS A 708 SG 115.7 REMARK 620 3 CYS A 723 SG 111.6 109.3 REMARK 620 4 CYS A 725 SG 105.9 101.2 112.7 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 ZN A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN 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 EDO A 810 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 811 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 812 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 813 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 814 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 815 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FQK A 816 DBREF 6H51 A 26 369 UNP Q9UGL1 KDM5B_HUMAN 26 101 DBREF 6H51 A 374 772 UNP Q9UGL1 KDM5B_HUMAN 374 772 SEQADV 6H51 SER A 24 UNP Q9UGL1 EXPRESSION TAG SEQADV 6H51 MET A 25 UNP Q9UGL1 EXPRESSION TAG SEQADV 6H51 GLY A 370 UNP Q9UGL1 LINKER SEQADV 6H51 GLY A 371 UNP Q9UGL1 LINKER SEQADV 6H51 GLY A 372 UNP Q9UGL1 LINKER SEQADV 6H51 GLY A 373 UNP Q9UGL1 LINKER SEQRES 1 A 481 SER MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU SEQRES 2 A 481 PRO SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE SEQRES 3 A 481 HIS LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS SEQRES 4 A 481 LYS VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA SEQRES 5 A 481 CYS ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN SEQRES 6 A 481 ARG LEU ASN GLU LEU GLU ALA GLN THR ARG VAL LYS LEU SEQRES 7 A 481 GLY GLY GLY GLY ALA ARG ASP TYR THR LEU ARG THR PHE SEQRES 8 A 481 GLY GLU MET ALA ASP ALA PHE LYS SER ASP TYR PHE ASN SEQRES 9 A 481 MET PRO VAL HIS MET VAL PRO THR GLU LEU VAL GLU LYS SEQRES 10 A 481 GLU PHE TRP ARG LEU VAL SER THR ILE GLU GLU ASP VAL SEQRES 11 A 481 THR VAL GLU TYR GLY ALA ASP ILE ALA SER LYS GLU PHE SEQRES 12 A 481 GLY SER GLY PHE PRO VAL ARG ASP GLY LYS ILE LYS LEU SEQRES 13 A 481 SER PRO GLU GLU GLU GLU TYR LEU ASP SER GLY TRP ASN SEQRES 14 A 481 LEU ASN ASN MET PRO VAL MET GLU GLN SER VAL LEU ALA SEQRES 15 A 481 HIS ILE THR ALA ASP ILE CYS GLY MET LYS LEU PRO TRP SEQRES 16 A 481 LEU TYR VAL GLY MET CYS PHE SER SER PHE CYS TRP HIS SEQRES 17 A 481 ILE GLU ASP HIS TRP SER TYR SER ILE ASN TYR LEU HIS SEQRES 18 A 481 TRP GLY GLU PRO LYS THR TRP TYR GLY VAL PRO GLY TYR SEQRES 19 A 481 ALA ALA GLU GLN LEU GLU ASN VAL MET LYS LYS LEU ALA SEQRES 20 A 481 PRO GLU LEU PHE VAL SER GLN PRO ASP LEU LEU HIS GLN SEQRES 21 A 481 LEU VAL THR ILE MET ASN PRO ASN THR LEU MET THR HIS SEQRES 22 A 481 GLU VAL PRO VAL TYR ARG THR ASN GLN CYS ALA GLY GLU SEQRES 23 A 481 PHE VAL ILE THR PHE PRO ARG ALA TYR HIS SER GLY PHE SEQRES 24 A 481 ASN GLN GLY PHE ASN PHE ALA GLU ALA VAL ASN PHE CYS SEQRES 25 A 481 THR VAL ASP TRP LEU PRO LEU GLY ARG GLN CYS VAL GLU SEQRES 26 A 481 HIS TYR ARG LEU LEU HIS ARG TYR CYS VAL PHE SER HIS SEQRES 27 A 481 ASP GLU MET ILE CYS LYS MET ALA SER LYS ALA ASP VAL SEQRES 28 A 481 LEU ASP VAL VAL VAL ALA SER THR VAL GLN LYS ASP MET SEQRES 29 A 481 ALA ILE MET ILE GLU ASP GLU LYS ALA LEU ARG GLU THR SEQRES 30 A 481 VAL ARG LYS LEU GLY VAL ILE ASP SER GLU ARG MET ASP SEQRES 31 A 481 PHE GLU LEU LEU PRO ASP ASP GLU ARG GLN CYS VAL LYS SEQRES 32 A 481 CYS LYS THR THR CYS PHE MET SER ALA ILE SER CYS SER SEQRES 33 A 481 CYS LYS PRO GLY LEU LEU VAL CYS LEU HIS HIS VAL LYS SEQRES 34 A 481 GLU LEU CYS SER CYS PRO PRO TYR LYS TYR LYS LEU ARG SEQRES 35 A 481 TYR ARG TYR THR LEU ASP ASP LEU TYR PRO MET MET ASN SEQRES 36 A 481 ALA LEU LYS LEU ARG ALA GLU SER TYR ASN GLU TRP ALA SEQRES 37 A 481 LEU ASN VAL ASN GLU ALA LEU GLU ALA LYS ILE ASN LYS HET ZN A 801 1 HET ZN A 802 1 HET MN A 803 1 HET MN A 804 1 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 EDO A 810 4 HET EDO A 811 4 HET EDO A 812 4 HET EDO A 813 4 HET EDO A 814 4 HET PO4 A 815 5 HET FQK A 816 23 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM PO4 PHOSPHATE ION HETNAM FQK 8-[4-[1-(CYCLOBUTYLMETHYL)PIPERIDIN-4-YL]PYRAZOL-1-YL]- HETNAM 2 FQK 3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN 2(ZN 2+) FORMUL 4 MN 2(MN 2+) FORMUL 6 DMS 5(C2 H6 O S) FORMUL 11 EDO 5(C2 H6 O2) FORMUL 16 PO4 O4 P 3- FORMUL 17 FQK C20 H24 N6 O FORMUL 18 HOH *282(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 402 THR A 416 1 15 HELIX 5 AA5 SER A 448 TYR A 454 1 7 HELIX 6 AA6 ASN A 463 MET A 467 5 5 HELIX 7 AA7 VAL A 471 ILE A 475 5 5 HELIX 8 AA8 ILE A 479 LEU A 484 1 6 HELIX 9 AA9 GLU A 501 SER A 505 5 5 HELIX 10 AB1 PRO A 523 TYR A 525 5 3 HELIX 11 AB2 ALA A 526 ALA A 538 1 13 HELIX 12 AB3 PRO A 539 PHE A 542 5 4 HELIX 13 AB4 ASP A 547 HIS A 550 5 4 HELIX 14 AB5 ASN A 557 HIS A 564 1 8 HELIX 15 AB6 THR A 604 ASP A 606 5 3 HELIX 16 AB7 TRP A 607 HIS A 622 1 16 HELIX 17 AB8 SER A 628 SER A 638 1 11 HELIX 18 AB9 LYS A 639 LEU A 643 5 5 HELIX 19 AC1 ASP A 644 LEU A 672 1 29 HELIX 20 AC2 ASP A 681 LEU A 685 5 5 HELIX 21 AC3 PRO A 686 ARG A 690 5 5 HELIX 22 AC4 HIS A 718 LEU A 722 5 5 HELIX 23 AC5 PRO A 726 TYR A 728 5 3 HELIX 24 AC6 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 TRP A 486 O ALA A 599 SHEET 7 AA1 8 THR A 422 ILE A 429 -1 N GLY A 426 O VAL A 489 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 GLY A 589 N PHE A 496 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 ASP A 676 ARG A 679 0 SHEET 2 AA5 3 TYR A 730 TYR A 734 1 O LEU A 732 N ASP A 676 SHEET 3 AA5 3 SER A 702 CYS A 706 -1 N ALA A 703 O ARG A 733 LINK O ALEU A 413 MN MN A 803 1555 1555 2.65 LINK O BLEU A 413 MN MN A 803 1555 1555 2.60 LINK O THR A 416 MN MN A 803 1555 1555 2.42 LINK NE2 HIS A 499 MN MN A 804 1555 1555 2.16 LINK OE2 GLU A 501 MN MN A 804 1555 1555 2.14 LINK NE2 HIS A 587 MN MN A 804 1555 1555 2.22 LINK SG CYS A 692 ZN ZN A 801 1555 1555 2.27 LINK SG CYS A 695 ZN ZN A 801 1555 1555 2.44 LINK SG CYS A 706 ZN ZN A 802 1555 1555 2.34 LINK SG CYS A 708 ZN ZN A 802 1555 1555 2.16 LINK SG CYS A 715 ZN ZN A 801 1555 1555 2.28 LINK ND1 HIS A 718 ZN ZN A 801 1555 1555 2.05 LINK SG CYS A 723 ZN ZN A 802 1555 1555 2.22 LINK SG CYS A 725 ZN ZN A 802 1555 1555 2.53 LINK MN MN A 804 N4 FQK A 816 1555 1555 1.86 LINK MN MN A 804 N FQK A 816 1555 1555 2.15 LINK MN MN A 804 N3 FQK A 816 1555 1555 2.71 LINK MN MN A 804 O HOH A 950 1555 1555 2.07 SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718 SITE 1 AC2 4 CYS A 706 CYS A 708 CYS A 723 CYS A 725 SITE 1 AC3 5 LEU A 90 ASN A 91 LEU A 413 THR A 416 SITE 2 AC3 5 GLU A 419 SITE 1 AC4 5 HIS A 499 GLU A 501 HIS A 587 FQK A 816 SITE 2 AC4 5 HOH A 950 SITE 1 AC5 8 TYR A 488 GLU A 501 SER A 507 ALA A 599 SITE 2 AC5 8 VAL A 600 ASN A 601 FQK A 816 HOH A 904 SITE 1 AC6 7 GLU A 631 CYS A 634 LYS A 635 GLU A 683 SITE 2 AC6 7 PHE A 700 ARG A 735 TYR A 736 SITE 1 AC7 2 HIS A 399 HOH A 925 SITE 1 AC8 4 SER A 677 LEU A 732 HOH A 940 HOH A1003 SITE 1 AC9 4 CYS A 497 VAL A 553 FQK A 816 HOH A 957 SITE 1 AD1 7 PHE A 83 GLY A 426 ALA A 427 ASP A 428 SITE 2 AD1 7 PHE A 434 LEU A 487 VAL A 489 SITE 1 AD2 3 VAL A 674 ILE A 675 HOH A 940 SITE 1 AD3 1 ARG A 679 SITE 1 AD4 2 GLY A 524 ARG A 584 SITE 1 AD5 1 HOH A1030 SITE 1 AD6 4 HIS A 622 LYS A 694 HIS A 718 HOH A 911 SITE 1 AD7 14 TYR A 425 TRP A 486 TYR A 488 PHE A 496 SITE 2 AD7 14 HIS A 499 GLU A 501 LYS A 517 TRP A 519 SITE 3 AD7 14 HIS A 587 MN A 804 DMS A 805 DMS A 809 SITE 4 AD7 14 HOH A 904 HOH A 950 CRYST1 142.000 142.000 152.410 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 0.007042 0.004066 0.000000 0.00000 SCALE2 0.000000 0.008132 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006561 0.00000