HEADER OXIDOREDUCTASE 09-OCT-15 5FJK TITLE CRYSTAL STRUCTURE OF HUMAN JMJD2C CATALYTIC DOMAIN IN COMPLEX 6-ETHYL- TITLE 2 5-METHYL-7-OXO-4,7-DIHYDROPYRAZOLO(1,5-A)PYRIMIDINE-3-CARBONITRILE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 3-347; COMPND 5 SYNONYM: JMJD2C, GENE AMPLIFIED IN SQUAMOUS CELL CARCINOMA 1 PROTEIN, COMPND 6 GASC-1 PROTEIN, JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN COMPND 7 3C, JUMONJI DOMAIN-CONTAINING PROTEIN 2C; COMPND 8 EC: 1.14.11.-; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETM14 KEYWDS OXIDOREDUCTASE, TRANSCRIPTION REGULATION, METAL BINDING, DEMETHYLASE, KEYWDS 2 LYSINE-SPECIFIC DEMETHYLASE 4C EXPDTA X-RAY DIFFRACTION AUTHOR V.CECATIELLO,S.PASQUALATO REVDAT 2 10-JAN-24 5FJK 1 REMARK REVDAT 1 21-OCT-15 5FJK 0 JRNL AUTH V.CECATIELLO,S.PASQUALATO JRNL TITL CRYSTAL STRUCTURES OF HUMAN JMJD2C CATALYTIC DOMAIN BOUND TO JRNL TITL 2 INHIBITORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 48144 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2341 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 53.8019 - 4.2677 1.00 2856 147 0.1419 0.1782 REMARK 3 2 4.2677 - 3.3875 0.99 2763 121 0.1331 0.1484 REMARK 3 3 3.3875 - 2.9594 1.00 2710 157 0.1575 0.1964 REMARK 3 4 2.9594 - 2.6888 1.00 2690 141 0.1688 0.2222 REMARK 3 5 2.6888 - 2.4961 1.00 2685 173 0.1636 0.2138 REMARK 3 6 2.4961 - 2.3489 1.00 2706 124 0.1594 0.2229 REMARK 3 7 2.3489 - 2.2313 1.00 2655 171 0.1537 0.1832 REMARK 3 8 2.2313 - 2.1341 1.00 2668 156 0.1588 0.1887 REMARK 3 9 2.1341 - 2.0520 1.00 2694 136 0.1628 0.2184 REMARK 3 10 2.0520 - 1.9812 1.00 2674 135 0.1719 0.2213 REMARK 3 11 1.9812 - 1.9192 1.00 2687 127 0.1691 0.2319 REMARK 3 12 1.9192 - 1.8644 1.00 2663 141 0.1762 0.1923 REMARK 3 13 1.8644 - 1.8153 1.00 2676 131 0.1829 0.2165 REMARK 3 14 1.8153 - 1.7710 1.00 2691 121 0.2011 0.2455 REMARK 3 15 1.7710 - 1.7307 0.99 2636 127 0.2118 0.2436 REMARK 3 16 1.7307 - 1.6939 0.99 2687 119 0.2411 0.2612 REMARK 3 17 1.6939 - 1.6600 0.99 2662 114 0.2662 0.3088 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 2871 REMARK 3 ANGLE : 1.185 3878 REMARK 3 CHIRALITY : 0.072 394 REMARK 3 PLANARITY : 0.008 493 REMARK 3 DIHEDRAL : 12.304 1682 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 10 THROUGH 295 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.9338 -22.4192 -6.1971 REMARK 3 T TENSOR REMARK 3 T11: 0.1513 T22: 0.1630 REMARK 3 T33: 0.1306 T12: 0.0141 REMARK 3 T13: 0.0064 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 2.1777 L22: 0.6505 REMARK 3 L33: 1.3096 L12: 0.6093 REMARK 3 L13: -0.3766 L23: -0.2806 REMARK 3 S TENSOR REMARK 3 S11: 0.0171 S12: -0.0464 S13: 0.0599 REMARK 3 S21: 0.0202 S22: -0.0330 S23: 0.0112 REMARK 3 S31: 0.0028 S32: -0.0680 S33: 0.0114 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 296 THROUGH 347 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.4314 -31.5834 14.9433 REMARK 3 T TENSOR REMARK 3 T11: 0.1849 T22: 0.2494 REMARK 3 T33: 0.1445 T12: 0.0115 REMARK 3 T13: 0.0022 T23: 0.0128 REMARK 3 L TENSOR REMARK 3 L11: 5.7416 L22: 4.8333 REMARK 3 L33: 5.0685 L12: -0.3257 REMARK 3 L13: 0.1551 L23: -0.1927 REMARK 3 S TENSOR REMARK 3 S11: -0.2087 S12: -0.1100 S13: -0.0839 REMARK 3 S21: 0.0371 S22: 0.1891 S23: -0.3018 REMARK 3 S31: 0.0702 S32: 0.2344 S33: 0.0360 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 5FJK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1290065264. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48173 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 53.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: PDB ENTRY 2XML REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 3350, 5% 1,2 ETHANEDIOL, 0.2 M REMARK 280 NANO3, 0.1 M BIS-TRIS PROPANE PH 7.25 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.49500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.49500 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 44.95000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.63500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 44.95000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.63500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.49500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 44.95000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.63500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.49500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 44.95000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.63500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 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 CL CL A1354 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2069 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2146 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2245 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 GLY A -1 REMARK 465 PRO A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 VAL A 3 REMARK 465 ALA A 4 REMARK 465 GLU A 5 REMARK 465 VAL A 6 REMARK 465 GLU A 7 REMARK 465 SER A 8 REMARK 465 PRO A 9 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 LYS A 53 CG CD CE NZ REMARK 470 GLU A 145 CG CD OE1 OE2 REMARK 470 GLU A 164 CG CD OE1 OE2 REMARK 470 LYS A 347 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2173 O HOH A 2338 2.06 REMARK 500 O HOH A 2152 O HOH A 2153 2.14 REMARK 500 O HOH A 2019 O HOH A 2037 2.16 REMARK 500 O HOH A 2171 O HOH A 2286 2.17 REMARK 500 O GLU A 24 O HOH A 2034 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 OE1 GLU A 28 O HOH A 2118 8445 1.95 REMARK 500 O HOH A 2158 O HOH A 2325 6444 2.10 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 PHE A 129 -118.87 -98.23 REMARK 500 ARG A 154 66.57 -155.33 REMARK 500 LYS A 184 1.71 82.05 REMARK 500 MET A 194 19.67 58.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 309 CYS A 310 -149.44 REMARK 500 REMARK 500 REMARK: NULL 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 1348 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1349 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EM6 A 1350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1351 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1352 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1353 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1354 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1355 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1356 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1357 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1358 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1359 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FJH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2C CATALYTIC DOMAIN IN COMPLEX WITH REMARK 900 EPITHERAPUETIC COMPOUND 2-(((2-((2-( DIMETHYLAMINO)ETHYL) (ETHYL) REMARK 900 AMINO)-2-OXOETHYL)AMINO) METHYL)ISONICOTINIC ACID DBREF 5FJK A 3 347 UNP Q9H3R0 KDM4C_HUMAN 3 347 SEQADV 5FJK GLY A -1 UNP Q9H3R0 EXPRESSION TAG SEQADV 5FJK PRO A 0 UNP Q9H3R0 EXPRESSION TAG SEQADV 5FJK MET A 1 UNP Q9H3R0 EXPRESSION TAG SEQADV 5FJK ASN A 2 UNP Q9H3R0 EXPRESSION TAG SEQRES 1 A 349 GLY PRO MET ASN VAL ALA GLU VAL GLU SER PRO LEU ASN SEQRES 2 A 349 PRO SER CYS LYS ILE MET THR PHE ARG PRO SER MET GLU SEQRES 3 A 349 GLU PHE ARG GLU PHE ASN LYS TYR LEU ALA TYR MET GLU SEQRES 4 A 349 SER LYS GLY ALA HIS ARG ALA GLY LEU ALA LYS VAL ILE SEQRES 5 A 349 PRO PRO LYS GLU TRP LYS PRO ARG GLN CYS TYR ASP ASP SEQRES 6 A 349 ILE ASP ASN LEU LEU ILE PRO ALA PRO ILE GLN GLN MET SEQRES 7 A 349 VAL THR GLY GLN SER GLY LEU PHE THR GLN TYR ASN ILE SEQRES 8 A 349 GLN LYS LYS ALA MET THR VAL LYS GLU PHE ARG GLN LEU SEQRES 9 A 349 ALA ASN SER GLY LYS TYR CYS THR PRO ARG TYR LEU ASP SEQRES 10 A 349 TYR GLU ASP LEU GLU ARG LYS TYR TRP LYS ASN LEU THR SEQRES 11 A 349 PHE VAL ALA PRO ILE TYR GLY ALA ASP ILE ASN GLY SER SEQRES 12 A 349 ILE TYR ASP GLU GLY VAL ASP GLU TRP ASN ILE ALA ARG SEQRES 13 A 349 LEU ASN THR VAL LEU ASP VAL VAL GLU GLU GLU CYS GLY SEQRES 14 A 349 ILE SER ILE GLU GLY VAL ASN THR PRO TYR LEU TYR PHE SEQRES 15 A 349 GLY MET TRP LYS THR THR PHE ALA TRP HIS THR GLU ASP SEQRES 16 A 349 MET ASP LEU TYR SER ILE ASN TYR LEU HIS PHE GLY GLU SEQRES 17 A 349 PRO LYS SER TRP TYR ALA ILE PRO PRO GLU HIS GLY LYS SEQRES 18 A 349 ARG LEU GLU ARG LEU ALA GLN GLY PHE PHE PRO SER SER SEQRES 19 A 349 SER GLN GLY CYS ASP ALA PHE LEU ARG HIS LYS MET THR SEQRES 20 A 349 LEU ILE SER PRO SER VAL LEU LYS LYS TYR GLY ILE PRO SEQRES 21 A 349 PHE ASP LYS ILE THR GLN GLU ALA GLY GLU PHE MET ILE SEQRES 22 A 349 THR PHE PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY SEQRES 23 A 349 PHE ASN CYS ALA GLU SER THR ASN PHE ALA THR VAL ARG SEQRES 24 A 349 TRP ILE ASP TYR GLY LYS VAL ALA LYS LEU CYS THR CYS SEQRES 25 A 349 ARG LYS ASP MET VAL LYS ILE SER MET ASP ILE PHE VAL SEQRES 26 A 349 ARG LYS PHE GLN PRO ASP ARG TYR GLN LEU TRP LYS GLN SEQRES 27 A 349 GLY LYS ASP ILE TYR THR ILE ASP HIS THR LYS HET ZN A1348 1 HET NI A1349 1 HET EM6 A1350 15 HET CL A1351 1 HET CL A1352 1 HET CL A1353 1 HET CL A1354 1 HET EDO A1355 4 HET EDO A1356 4 HET EDO A1357 4 HET EDO A1358 4 HET EDO A1359 4 HETNAM ZN ZINC ION HETNAM NI NICKEL (II) ION HETNAM EM6 6-ETHYL-5-METHYL-7-OXIDANYLIDENE-1H-PYRAZOLO[1,5- HETNAM 2 EM6 A]PYRIMIDINE-3-CARBONITRILE HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 NI NI 2+ FORMUL 4 EM6 C10 H10 N4 O FORMUL 5 CL 4(CL 1-) FORMUL 9 EDO 5(C2 H6 O2) FORMUL 14 HOH *350(H2 O) HELIX 1 1 SER A 22 ARG A 27 1 6 HELIX 2 2 GLU A 28 LYS A 39 1 12 HELIX 3 3 GLY A 40 ALA A 44 5 5 HELIX 4 4 TYR A 61 ASN A 66 5 6 HELIX 5 5 VAL A 96 ASN A 104 1 9 HELIX 6 6 ASP A 115 LEU A 127 1 13 HELIX 7 7 THR A 157 GLY A 167 1 11 HELIX 8 8 GLU A 192 LEU A 196 5 5 HELIX 9 9 PRO A 214 GLU A 216 5 3 HELIX 10 10 HIS A 217 PHE A 229 1 13 HELIX 11 11 PHE A 229 CYS A 236 1 8 HELIX 12 12 ALA A 238 LYS A 243 5 6 HELIX 13 13 SER A 248 GLY A 256 1 9 HELIX 14 14 THR A 295 ARG A 297 5 3 HELIX 15 15 TRP A 298 ALA A 305 1 8 HELIX 16 16 MET A 319 GLN A 327 1 9 HELIX 17 17 ARG A 330 GLN A 336 1 7 SHEET 1 AA10 MET A 17 PHE A 19 0 SHEET 2 AA10 LEU A 46 VAL A 49 1 O LEU A 46 N MET A 17 SHEET 3 AA10 PHE A 269 THR A 272 -1 O PHE A 269 N VAL A 49 SHEET 4 AA10 TYR A 197 GLY A 205 -1 O SER A 198 N THR A 272 SHEET 5 AA10 ASN A 286 PHE A 293 -1 O CYS A 287 N HIS A 203 SHEET 6 AA10 TYR A 177 GLY A 181 -1 O TYR A 177 N SER A 290 SHEET 7 AA10 ILE A 133 ASN A 139 -1 O GLY A 135 N PHE A 180 SHEET 8 AA10 ILE A 73 GLN A 80 -1 O ILE A 73 N TYR A 134 SHEET 9 AA10 LEU A 83 GLN A 90 -1 O LEU A 83 N GLN A 80 SHEET 10 AA10 THR A 245 ILE A 247 -1 O LEU A 246 N PHE A 84 SHEET 1 AB 2 LEU A 68 ILE A 69 0 SHEET 2 AB 2 MET A 94 THR A 95 -1 O MET A 94 N ILE A 69 SHEET 1 AC 4 THR A 186 HIS A 190 0 SHEET 2 AC 4 TYR A 277 ASN A 282 -1 O HIS A 278 N HIS A 190 SHEET 3 AC 4 LYS A 208 ILE A 213 -1 O SER A 209 N PHE A 281 SHEET 4 AC 4 ASP A 260 GLN A 264 -1 O ASP A 260 N ALA A 212 LINK NI NI A1349 N10 EM6 A1350 1555 1555 2.25 SITE 1 AC1 4 CYS A 236 HIS A 242 CYS A 308 CYS A 310 SITE 1 AC2 6 HIS A 190 GLU A 192 HIS A 278 EM6 A1350 SITE 2 AC2 6 HOH A2221 HOH A2227 SITE 1 AC3 12 TYR A 134 THR A 186 PHE A 187 HIS A 190 SITE 2 AC3 12 ASN A 200 LYS A 208 HIS A 278 ASN A 282 SITE 3 AC3 12 NI A1349 HOH A2221 HOH A2227 HOH A2346 SITE 1 AC4 3 ARG A 112 ASN A 126 TRP A 183 SITE 1 AC5 2 TYR A 179 SER A 290 SITE 1 AC6 4 ALA A 238 PHE A 239 LEU A 240 HOH A2264 SITE 1 AC7 2 PRO A 111 ARG A 112 SITE 1 AC8 5 ASN A 88 GLN A 90 EDO A1356 HOH A2347 SITE 2 AC8 5 HOH A2348 SITE 1 AC9 2 GLN A 90 EDO A1355 SITE 1 BC1 5 LYS A 56 GLU A 149 HOH A2078 HOH A2349 SITE 2 BC1 5 HOH A2350 SITE 1 BC2 6 TYR A 116 GLU A 117 GLU A 120 SER A 209 SITE 2 BC2 6 LYS A 261 HOH A2288 SITE 1 BC3 5 LYS A 107 GLN A 327 PRO A 328 ASP A 329 SITE 2 BC3 5 HOH A2335 CRYST1 89.900 91.270 98.990 90.00 90.00 90.00 C 2 2 21 8 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 0.011123 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010957 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010102 0.00000