HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 31-JUL-20 7JM5 TITLE CRYSTAL STRUCTURE OF KDM4B IN COMPLEX WITH QC6352 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4B; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3B, COMPND 5 JUMONJI DOMAIN-CONTAINING PROTEIN 2B,[HISTONE H3]-TRIMETHYL-L- COMPND 6 LYSINE(9) DEMETHYLASE 4B; COMPND 7 EC: 1.14.11.66; COMPND 8 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: KDM4B, JHDM3B, JMJD2B, KIAA0876; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KDM4, KDM4B, PROTEIN-INHIBITOR COMPLEX, DEMETHYLASE, EPIGENETICS, KEYWDS 2 OXIDOREDUCTASE-INHIBITOR COMPLEX, OXIDOREDUCTASE, OXIDOREDUCTASE- KEYWDS 3 OXIDOREDUCTASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.W.WHITE,M.YUN REVDAT 3 18-OCT-23 7JM5 1 REMARK REVDAT 2 17-AUG-22 7JM5 1 JRNL REVDAT 1 02-FEB-22 7JM5 0 JRNL AUTH S.SINGH,A.ABU-ZAID,H.JIN,J.FANG,Q.WU,T.WANG,H.FENG,W.QUARNI, JRNL AUTH 2 Y.SHAO,L.MAXHAM,A.ABDOLVAHABI,M.K.YUN,S.VAITHIYALINGAM, JRNL AUTH 3 H.TAN,J.BOWLING,V.HONNELL,B.YOUNG,Y.GUO,R.BAJPAI, JRNL AUTH 4 S.M.PRUETT-MILLER,G.C.GROSVELD,M.HATLEY,B.XU,Y.FAN,G.WU, JRNL AUTH 5 E.Y.CHEN,T.CHEN,P.W.LEWIS,Z.RANKOVIC,Y.LI,A.J.MURPHY, JRNL AUTH 6 J.EASTON,J.PENG,X.CHEN,R.WANG,S.W.WHITE,A.M.DAVIDOFF,J.YANG JRNL TITL TARGETING KDM4 FOR TREATING PAX3-FOXO1-DRIVEN ALVEOLAR JRNL TITL 2 RHABDOMYOSARCOMA. JRNL REF SCI TRANSL MED V. 14 Q2096 2022 JRNL REFN ESSN 1946-6242 JRNL PMID 35857643 JRNL DOI 10.1126/SCITRANSLMED.ABQ2096 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 24053 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1201 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 41.0300 - 5.6100 0.99 2595 137 0.1788 0.2299 REMARK 3 2 5.6100 - 4.4600 1.00 2565 135 0.1552 0.1981 REMARK 3 3 4.4600 - 3.8900 1.00 2545 134 0.1659 0.2223 REMARK 3 4 3.8900 - 3.5400 1.00 2547 134 0.1971 0.2694 REMARK 3 5 3.5400 - 3.2800 1.00 2545 134 0.2218 0.2471 REMARK 3 6 3.2800 - 3.0900 1.00 2530 134 0.2277 0.2779 REMARK 3 7 3.0900 - 2.9400 1.00 2554 133 0.2675 0.2994 REMARK 3 8 2.9400 - 2.8100 0.99 2511 132 0.2911 0.3181 REMARK 3 9 2.8100 - 2.7000 0.96 2460 128 0.3310 0.3655 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) : 0.383 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 64.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.42 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 : 0.002 5768 REMARK 3 ANGLE : 0.476 7829 REMARK 3 CHIRALITY : 0.043 814 REMARK 3 PLANARITY : 0.004 994 REMARK 3 DIHEDRAL : 11.407 3366 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 6 THROUGH 362) REMARK 3 ORIGIN FOR THE GROUP (A): 64.9747 -3.2885 25.6252 REMARK 3 T TENSOR REMARK 3 T11: 0.6046 T22: 0.4854 REMARK 3 T33: 0.4624 T12: -0.0574 REMARK 3 T13: -0.0609 T23: -0.0228 REMARK 3 L TENSOR REMARK 3 L11: 1.1369 L22: 2.8941 REMARK 3 L33: 1.8600 L12: -0.3321 REMARK 3 L13: 0.5948 L23: -0.4605 REMARK 3 S TENSOR REMARK 3 S11: -0.0514 S12: -0.0295 S13: 0.0357 REMARK 3 S21: 0.1815 S22: 0.0148 S23: 0.1020 REMARK 3 S31: -0.1448 S32: -0.0736 S33: 0.0367 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 7 THROUGH 362) REMARK 3 ORIGIN FOR THE GROUP (A): 42.0852 -2.7889 -10.2598 REMARK 3 T TENSOR REMARK 3 T11: 0.5199 T22: 0.5215 REMARK 3 T33: 0.5194 T12: -0.0546 REMARK 3 T13: -0.0678 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 1.8484 L22: 2.6285 REMARK 3 L33: 3.4513 L12: -0.7455 REMARK 3 L13: -1.2777 L23: 1.0292 REMARK 3 S TENSOR REMARK 3 S11: -0.0007 S12: 0.0957 S13: 0.0644 REMARK 3 S21: 0.2477 S22: -0.0431 S23: 0.2335 REMARK 3 S31: 0.1769 S32: -0.3280 S33: 0.0345 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 501) REMARK 3 ORIGIN FOR THE GROUP (A): 63.7907 -10.2030 19.8725 REMARK 3 T TENSOR REMARK 3 T11: 1.0829 T22: 0.8307 REMARK 3 T33: 1.1210 T12: -0.0276 REMARK 3 T13: -0.2298 T23: 0.2328 REMARK 3 L TENSOR REMARK 3 L11: 4.2650 L22: 4.3964 REMARK 3 L33: 8.2145 L12: -0.3208 REMARK 3 L13: -1.7216 L23: -0.3356 REMARK 3 S TENSOR REMARK 3 S11: 0.0554 S12: 0.3396 S13: 0.1833 REMARK 3 S21: -0.4495 S22: -0.0792 S23: 0.2189 REMARK 3 S31: -0.1360 S32: 0.0187 S33: 0.0188 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 501) REMARK 3 ORIGIN FOR THE GROUP (A): 48.2073 -8.7106 -7.8967 REMARK 3 T TENSOR REMARK 3 T11: 1.1017 T22: 0.9904 REMARK 3 T33: 0.9023 T12: -0.1091 REMARK 3 T13: -0.2517 T23: 0.1061 REMARK 3 L TENSOR REMARK 3 L11: 1.4986 L22: 2.1125 REMARK 3 L33: 3.0303 L12: -0.2609 REMARK 3 L13: 1.5176 L23: -2.0186 REMARK 3 S TENSOR REMARK 3 S11: -0.1944 S12: -0.2652 S13: 0.1314 REMARK 3 S21: 0.1395 S22: 0.1953 S23: 0.3309 REMARK 3 S31: -0.0944 S32: 0.0836 S33: -0.0091 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 7JM5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251038. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24351 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.12500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.76300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: 4LXL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRI-SODIUM CITRATE, PEG 3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 48.55350 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 SER A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 GLU A 4 REMARK 465 ASP A 5 REMARK 465 SER A 231 REMARK 465 SER A 232 REMARK 465 GLN A 233 REMARK 465 GLY A 234 REMARK 465 CYS A 235 REMARK 465 ASP A 236 REMARK 465 GLN A 306 REMARK 465 CYS A 307 REMARK 465 THR A 308 REMARK 465 CYS A 309 REMARK 465 ARG A 310 REMARK 465 LYS A 311 REMARK 465 ASP A 312 REMARK 465 MET A 313 REMARK 465 ALA A 363 REMARK 465 SER A 364 REMARK 465 LEU A 365 REMARK 465 LYS A 366 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 SER B 3 REMARK 465 GLU B 4 REMARK 465 ASP B 5 REMARK 465 HIS B 6 REMARK 465 GLY B 230 REMARK 465 SER B 231 REMARK 465 SER B 232 REMARK 465 GLN B 233 REMARK 465 GLY B 234 REMARK 465 CYS B 235 REMARK 465 ASP B 236 REMARK 465 ALA B 237 REMARK 465 THR B 305 REMARK 465 GLN B 306 REMARK 465 CYS B 307 REMARK 465 THR B 308 REMARK 465 CYS B 309 REMARK 465 ARG B 310 REMARK 465 LYS B 311 REMARK 465 ASP B 312 REMARK 465 MET B 313 REMARK 465 ALA B 363 REMARK 465 SER B 364 REMARK 465 LEU B 365 REMARK 465 LYS B 366 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 HIS A 6 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 163 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 240 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 362 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 337 CG CD CE NZ REMARK 470 ARG B 362 CG CD NE CZ NH1 NH2 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 SER A 153 82.19 -156.83 REMARK 500 PRO A 229 77.37 -69.54 REMARK 500 MET A 243 36.91 -150.59 REMARK 500 VAL B 172 -62.36 -104.72 REMARK 500 LYS B 183 -2.24 76.77 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 NI A 401 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 189 NE2 REMARK 620 2 GLU A 191 OE2 90.1 REMARK 620 3 HIS A 277 NE2 91.6 92.9 REMARK 620 4 9DJ A 402 N4 100.2 157.5 106.6 REMARK 620 5 HOH A 501 O 95.4 74.0 165.2 85.1 REMARK 620 6 HOH A 503 O 159.8 85.9 108.4 77.6 64.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 401 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 189 NE2 REMARK 620 2 GLU B 191 OE2 96.1 REMARK 620 3 HIS B 277 NE2 85.4 78.8 REMARK 620 4 9DJ B 403 N4 97.2 164.0 111.0 REMARK 620 5 HOH B 501 O 175.1 88.0 92.9 79.1 REMARK 620 6 HOH B 502 O 108.3 88.4 162.4 79.1 74.4 REMARK 620 N 1 2 3 4 5 DBREF 7JM5 A 1 366 UNP O94953 KDM4B_HUMAN 1 366 DBREF 7JM5 B 1 366 UNP O94953 KDM4B_HUMAN 1 366 SEQADV 7JM5 SER A 0 UNP O94953 EXPRESSION TAG SEQADV 7JM5 SER B 0 UNP O94953 EXPRESSION TAG SEQRES 1 A 367 SER MET GLY SER GLU ASP HIS GLY ALA GLN ASN PRO SER SEQRES 2 A 367 CYS LYS ILE MET THR PHE ARG PRO THR MET GLU GLU PHE SEQRES 3 A 367 LYS ASP PHE ASN LYS TYR VAL ALA TYR ILE GLU SER GLN SEQRES 4 A 367 GLY ALA HIS ARG ALA GLY LEU ALA LYS ILE ILE PRO PRO SEQRES 5 A 367 LYS GLU TRP LYS PRO ARG GLN THR TYR ASP ASP ILE ASP SEQRES 6 A 367 ASP VAL VAL ILE PRO ALA PRO ILE GLN GLN VAL VAL THR SEQRES 7 A 367 GLY GLN SER GLY LEU PHE THR GLN TYR ASN ILE GLN LYS SEQRES 8 A 367 LYS ALA MET THR VAL GLY GLU TYR ARG ARG LEU ALA ASN SEQRES 9 A 367 SER GLU LYS TYR CYS THR PRO ARG HIS GLN ASP PHE ASP SEQRES 10 A 367 ASP LEU GLU ARG LYS TYR TRP LYS ASN LEU THR PHE VAL SEQRES 11 A 367 SER PRO ILE TYR GLY ALA ASP ILE SER GLY SER LEU TYR SEQRES 12 A 367 ASP ASP ASP VAL ALA GLN TRP ASN ILE GLY SER LEU ARG SEQRES 13 A 367 THR ILE LEU ASP MET VAL GLU ARG GLU CYS GLY THR ILE SEQRES 14 A 367 ILE GLU GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET SEQRES 15 A 367 TRP LYS THR THR PHE ALA TRP HIS THR GLU ASP MET ASP SEQRES 16 A 367 LEU TYR SER ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SEQRES 17 A 367 SER TRP TYR ALA ILE PRO PRO GLU HIS GLY LYS ARG LEU SEQRES 18 A 367 GLU ARG LEU ALA ILE GLY PHE PHE PRO GLY SER SER GLN SEQRES 19 A 367 GLY CYS ASP ALA PHE LEU ARG HIS LYS MET THR LEU ILE SEQRES 20 A 367 SER PRO ILE ILE LEU LYS LYS TYR GLY ILE PRO PHE SER SEQRES 21 A 367 ARG ILE THR GLN GLU ALA GLY GLU PHE MET ILE THR PHE SEQRES 22 A 367 PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN SEQRES 23 A 367 CYS ALA GLU SER THR ASN PHE ALA THR LEU ARG TRP ILE SEQRES 24 A 367 ASP TYR GLY LYS VAL ALA THR GLN CYS THR CYS ARG LYS SEQRES 25 A 367 ASP MET VAL LYS ILE SER MET ASP VAL PHE VAL ARG ILE SEQRES 26 A 367 LEU GLN PRO GLU ARG TYR GLU LEU TRP LYS GLN GLY LYS SEQRES 27 A 367 ASP LEU THR VAL LEU ASP HIS THR ARG PRO THR ALA LEU SEQRES 28 A 367 THR SER PRO GLU LEU SER SER TRP SER ALA SER ARG ALA SEQRES 29 A 367 SER LEU LYS SEQRES 1 B 367 SER MET GLY SER GLU ASP HIS GLY ALA GLN ASN PRO SER SEQRES 2 B 367 CYS LYS ILE MET THR PHE ARG PRO THR MET GLU GLU PHE SEQRES 3 B 367 LYS ASP PHE ASN LYS TYR VAL ALA TYR ILE GLU SER GLN SEQRES 4 B 367 GLY ALA HIS ARG ALA GLY LEU ALA LYS ILE ILE PRO PRO SEQRES 5 B 367 LYS GLU TRP LYS PRO ARG GLN THR TYR ASP ASP ILE ASP SEQRES 6 B 367 ASP VAL VAL ILE PRO ALA PRO ILE GLN GLN VAL VAL THR SEQRES 7 B 367 GLY GLN SER GLY LEU PHE THR GLN TYR ASN ILE GLN LYS SEQRES 8 B 367 LYS ALA MET THR VAL GLY GLU TYR ARG ARG LEU ALA ASN SEQRES 9 B 367 SER GLU LYS TYR CYS THR PRO ARG HIS GLN ASP PHE ASP SEQRES 10 B 367 ASP LEU GLU ARG LYS TYR TRP LYS ASN LEU THR PHE VAL SEQRES 11 B 367 SER PRO ILE TYR GLY ALA ASP ILE SER GLY SER LEU TYR SEQRES 12 B 367 ASP ASP ASP VAL ALA GLN TRP ASN ILE GLY SER LEU ARG SEQRES 13 B 367 THR ILE LEU ASP MET VAL GLU ARG GLU CYS GLY THR ILE SEQRES 14 B 367 ILE GLU GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET SEQRES 15 B 367 TRP LYS THR THR PHE ALA TRP HIS THR GLU ASP MET ASP SEQRES 16 B 367 LEU TYR SER ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SEQRES 17 B 367 SER TRP TYR ALA ILE PRO PRO GLU HIS GLY LYS ARG LEU SEQRES 18 B 367 GLU ARG LEU ALA ILE GLY PHE PHE PRO GLY SER SER GLN SEQRES 19 B 367 GLY CYS ASP ALA PHE LEU ARG HIS LYS MET THR LEU ILE SEQRES 20 B 367 SER PRO ILE ILE LEU LYS LYS TYR GLY ILE PRO PHE SER SEQRES 21 B 367 ARG ILE THR GLN GLU ALA GLY GLU PHE MET ILE THR PHE SEQRES 22 B 367 PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN SEQRES 23 B 367 CYS ALA GLU SER THR ASN PHE ALA THR LEU ARG TRP ILE SEQRES 24 B 367 ASP TYR GLY LYS VAL ALA THR GLN CYS THR CYS ARG LYS SEQRES 25 B 367 ASP MET VAL LYS ILE SER MET ASP VAL PHE VAL ARG ILE SEQRES 26 B 367 LEU GLN PRO GLU ARG TYR GLU LEU TRP LYS GLN GLY LYS SEQRES 27 B 367 ASP LEU THR VAL LEU ASP HIS THR ARG PRO THR ALA LEU SEQRES 28 B 367 THR SER PRO GLU LEU SER SER TRP SER ALA SER ARG ALA SEQRES 29 B 367 SER LEU LYS HET NI A 401 1 HET 9DJ A 402 29 HET NI B 401 1 HET ZN B 402 1 HET 9DJ B 403 29 HETNAM NI NICKEL (II) ION HETNAM 9DJ 3-[({(1R)-6-[METHYL(PHENYL)AMINO]-1,2,3,4- HETNAM 2 9DJ TETRAHYDRONAPHTHALEN-1-YL}METHYL)AMINO]PYRIDINE-4- HETNAM 3 9DJ CARBOXYLIC ACID HETNAM ZN ZINC ION FORMUL 3 NI 2(NI 2+) FORMUL 4 9DJ 2(C24 H25 N3 O2) FORMUL 6 ZN ZN 2+ FORMUL 8 HOH *31(H2 O) HELIX 1 AA1 THR A 21 LYS A 26 1 6 HELIX 2 AA2 ASP A 27 GLN A 38 1 12 HELIX 3 AA3 GLY A 39 ALA A 43 5 5 HELIX 4 AA4 ASP A 62 ASP A 65 5 4 HELIX 5 AA5 VAL A 95 ASN A 103 1 9 HELIX 6 AA6 ASP A 114 ASN A 125 1 12 HELIX 7 AA7 LEU A 158 CYS A 165 1 8 HELIX 8 AA8 GLU A 191 LEU A 195 5 5 HELIX 9 AA9 PRO A 213 GLU A 215 5 3 HELIX 10 AB1 HIS A 216 PHE A 228 1 13 HELIX 11 AB2 ALA A 237 LYS A 242 5 6 HELIX 12 AB3 SER A 247 GLY A 255 1 9 HELIX 13 AB4 ARG A 296 ALA A 304 1 9 HELIX 14 AB5 MET A 318 GLN A 326 1 9 HELIX 15 AB6 ARG A 329 GLN A 335 1 7 HELIX 16 AB7 SER A 352 SER A 361 1 10 HELIX 17 AB8 THR B 21 LYS B 26 1 6 HELIX 18 AB9 ASP B 27 GLN B 38 1 12 HELIX 19 AC1 GLY B 39 ALA B 43 5 5 HELIX 20 AC2 VAL B 95 ASN B 103 1 9 HELIX 21 AC3 ASP B 114 ASN B 125 1 12 HELIX 22 AC4 LEU B 158 GLY B 166 1 9 HELIX 23 AC5 GLU B 191 LEU B 195 5 5 HELIX 24 AC6 PRO B 213 GLU B 215 5 3 HELIX 25 AC7 HIS B 216 ILE B 225 1 10 HELIX 26 AC8 PHE B 238 LYS B 242 5 5 HELIX 27 AC9 SER B 247 TYR B 254 1 8 HELIX 28 AD1 ARG B 296 VAL B 303 1 8 HELIX 29 AD2 MET B 318 LEU B 325 1 8 HELIX 30 AD3 GLN B 326 GLU B 328 5 3 HELIX 31 AD4 ARG B 329 GLN B 335 1 7 HELIX 32 AD5 SER B 352 ALA B 360 1 9 SHEET 1 AA110 THR A 17 PHE A 18 0 SHEET 2 AA110 LEU A 45 ILE A 48 1 O LYS A 47 N PHE A 18 SHEET 3 AA110 PHE A 268 THR A 271 -1 O PHE A 268 N ILE A 48 SHEET 4 AA110 TYR A 196 GLY A 204 -1 N ASN A 199 O MET A 269 SHEET 5 AA110 ASN A 285 PHE A 292 -1 O GLU A 288 N TYR A 200 SHEET 6 AA110 TYR A 176 GLY A 180 -1 N TYR A 176 O SER A 289 SHEET 7 AA110 ILE A 132 SER A 138 -1 N GLY A 134 O PHE A 179 SHEET 8 AA110 ILE A 72 GLN A 79 -1 N ILE A 72 O TYR A 133 SHEET 9 AA110 LEU A 82 GLN A 89 -1 O ILE A 88 N GLN A 73 SHEET 10 AA110 THR A 244 ILE A 246 -1 O LEU A 245 N PHE A 83 SHEET 1 AA2 2 VAL A 67 ILE A 68 0 SHEET 2 AA2 2 MET A 93 THR A 94 -1 O MET A 93 N ILE A 68 SHEET 1 AA3 4 THR A 185 HIS A 189 0 SHEET 2 AA3 4 TYR A 276 ASN A 281 -1 O GLY A 279 N PHE A 186 SHEET 3 AA3 4 LYS A 207 ILE A 212 -1 N TYR A 210 O ALA A 278 SHEET 4 AA3 4 SER A 259 GLN A 263 -1 O GLN A 263 N LYS A 207 SHEET 1 AA410 MET B 16 PHE B 18 0 SHEET 2 AA410 LEU B 45 ILE B 48 1 O LYS B 47 N PHE B 18 SHEET 3 AA410 PHE B 268 THR B 271 -1 O ILE B 270 N ALA B 46 SHEET 4 AA410 TYR B 196 GLY B 204 -1 N ASN B 199 O MET B 269 SHEET 5 AA410 ASN B 285 PHE B 292 -1 O GLU B 288 N TYR B 200 SHEET 6 AA410 TYR B 176 GLY B 180 -1 N TYR B 176 O SER B 289 SHEET 7 AA410 ILE B 132 SER B 138 -1 N GLY B 134 O PHE B 179 SHEET 8 AA410 ILE B 72 GLN B 79 -1 N ILE B 72 O TYR B 133 SHEET 9 AA410 LEU B 82 GLN B 89 -1 O ILE B 88 N GLN B 73 SHEET 10 AA410 THR B 244 ILE B 246 -1 O LEU B 245 N PHE B 83 SHEET 1 AA5 2 VAL B 67 ILE B 68 0 SHEET 2 AA5 2 MET B 93 THR B 94 -1 O MET B 93 N ILE B 68 SHEET 1 AA6 4 THR B 185 HIS B 189 0 SHEET 2 AA6 4 HIS B 277 ASN B 281 -1 O GLY B 279 N PHE B 186 SHEET 3 AA6 4 LYS B 207 ALA B 211 -1 N TYR B 210 O ALA B 278 SHEET 4 AA6 4 SER B 259 GLN B 263 -1 O ILE B 261 N TRP B 209 SSBOND 1 CYS A 165 CYS B 165 1555 1555 2.03 LINK NE2 HIS A 189 NI NI A 401 1555 1555 1.97 LINK OE2 GLU A 191 NI NI A 401 1555 1555 1.98 LINK NE2 HIS A 277 NI NI A 401 1555 1555 1.97 LINK NI NI A 401 N4 9DJ A 402 1555 1555 1.98 LINK NI NI A 401 O HOH A 501 1555 1555 2.23 LINK NI NI A 401 O HOH A 503 1555 1555 2.33 LINK NE2 HIS B 189 NI NI B 401 1555 1555 1.98 LINK OE2 GLU B 191 NI NI B 401 1555 1555 1.97 LINK NE2 HIS B 241 ZN ZN B 402 1555 1555 2.02 LINK NE2 HIS B 277 NI NI B 401 1555 1555 1.97 LINK NI NI B 401 N4 9DJ B 403 1555 1555 1.96 LINK NI NI B 401 O HOH B 501 1555 1555 2.02 LINK NI NI B 401 O HOH B 502 1555 1555 2.36 CRYST1 59.825 97.107 80.068 90.00 106.52 90.00 P 1 21 1 4 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 0.016715 0.000000 0.004956 0.00000 SCALE2 0.000000 0.010298 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013027 0.00000