HEADER OXIDOREDUCTASE 29-NOV-17 6F4N TITLE HUMAN JMJD5 IN COMPLEX WITH MN AND 2OG. COMPND MOL_ID: 1; COMPND 2 MOLECULE: JMJC DOMAIN-CONTAINING PROTEIN 5; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LYSINE-SPECIFIC DEMETHYLASE 8, JUMONJI DOMAIN-CONTAINING COMPND 5 PROTEIN 5; COMPND 6 EC: 1.14.11.47; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: CATALYTIC DOMAIN (RESIDUES 153-416) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDM8, JMJD5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNH-TRXT KEYWDS OXIDOREDUCTASE, NON-HEME, IRON, 2-OXOGLUTARATE, DIOXYGENASE, JMJC, KEYWDS 2 JMJC DOMAIN, LYSINE-SPECIFIC DEMETHYLASE 8, JMJC DOMAIN-CONTAINING KEYWDS 3 PROTEIN 5, ARGINYL C-3 HYDROXYLASE, JMJD5, KDM8, OXYGENASE, HYPOXIA, KEYWDS 4 DNA-BINDING, METAL-BINDING, TRANSLATION, DSBH, FACIAL TRIAD, KEYWDS 5 CYTOPLASM, JMJC HYDROXYLASE, JMJC DEMETHYLASE, KDMS, POST- KEYWDS 6 TRANSLATIONAL MODIFICATIONS, PTM, BETA-HYDROXYLATION, HYDROXYLATION, KEYWDS 7 ARGININE HYDROXYLATION, RCC1 DOMAIN-CONTAINING PROTEIN 1, RCCD1, KEYWDS 8 REGULATOR OF CHROMOSOME CONDENSATION, 40S RIBOSOMAL PROTEIN S6, KEYWDS 9 RPS6, RIBOSOME BIOGENESIS, TRANSCRIPTION, EPIGENETIC REGULATION, KEYWDS 10 SIGNALING, DEVELOPMENT, CELL STRUCTURE, TRANSCRIPTION KEYWDS 11 ACTIVATOR/INHIBITOR, PHOSPHORYLATION, CANCER, POLYMORPHISM EXPDTA X-RAY DIFFRACTION AUTHOR R.CHOWDHURY,M.S.ISLAM,C.J.SCHOFIELD REVDAT 3 16-OCT-24 6F4N 1 REMARK REVDAT 2 17-JAN-24 6F4N 1 LINK REVDAT 1 04-APR-18 6F4N 0 JRNL AUTH S.E.WILKINS,S.ISLAM,J.M.GANNON,S.MARKOLOVIC,R.J.HOPKINSON, JRNL AUTH 2 W.GE,C.J.SCHOFIELD,R.CHOWDHURY JRNL TITL JMJD5 IS A HUMAN ARGINYL C-3 HYDROXYLASE. JRNL REF NAT COMMUN V. 9 1180 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29563586 JRNL DOI 10.1038/S41467-018-03410-W REMARK 2 REMARK 2 RESOLUTION. 2.54 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) : 2.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 24595 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1242 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 49.1722 - 5.2845 1.00 2804 146 0.2005 0.2567 REMARK 3 2 5.2845 - 4.1951 1.00 2680 118 0.1545 0.1707 REMARK 3 3 4.1951 - 3.6650 1.00 2606 132 0.1744 0.1921 REMARK 3 4 3.6650 - 3.3300 1.00 2565 160 0.2007 0.2036 REMARK 3 5 3.3300 - 3.0914 1.00 2561 144 0.2222 0.2597 REMARK 3 6 3.0914 - 2.9091 0.99 2596 119 0.2466 0.2995 REMARK 3 7 2.9091 - 2.7635 1.00 2526 161 0.2762 0.2760 REMARK 3 8 2.7635 - 2.6432 0.99 2512 142 0.3003 0.3065 REMARK 3 9 2.6432 - 2.5414 0.98 2503 120 0.3301 0.3467 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 : 0.30 REMARK 3 B_SOL : 55.80 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.21000 REMARK 3 B22 (A**2) : 9.21000 REMARK 3 B33 (A**2) : -18.42000 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 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 : 0.005 4140 REMARK 3 ANGLE : 0.877 5658 REMARK 3 CHIRALITY : 0.061 597 REMARK 3 PLANARITY : 0.007 742 REMARK 3 DIHEDRAL : 17.539 2458 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT TARGET: ML AND BULK SOLVENT REMARK 3 MODELLING METHOD USED: FLAT MODEL REMARK 4 REMARK 4 6F4N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007737. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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) : 0.9795 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 706E REMARK 200 DATA SCALING SOFTWARE : HKL-2000 706E REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24683 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.540 REMARK 200 RESOLUTION RANGE LOW (A) : 49.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 1.10000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: 4GJZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.0, 21.4 % PEG3350, REMARK 280 0.07 M MGCL2, 0.002 M MNCL2, 300 NL SITTING DROPS (SAMPLE:WELL, REMARK 280 1:2 RATIO), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 178.59867 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 89.29933 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 89.29933 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 178.59867 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 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 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 GLU A 146 REMARK 465 ASN A 147 REMARK 465 LEU A 148 REMARK 465 TYR A 149 REMARK 465 PHE A 150 REMARK 465 GLN A 151 REMARK 465 SER A 152 REMARK 465 ARG A 153 REMARK 465 PRO A 154 REMARK 465 ALA A 155 REMARK 465 ARG A 156 REMARK 465 GLY A 157 REMARK 465 SER A 158 REMARK 465 LEU A 159 REMARK 465 PRO A 160 REMARK 465 GLU A 161 REMARK 465 GLN A 162 REMARK 465 PRO A 163 REMARK 465 CYS A 164 REMARK 465 THR A 165 REMARK 465 LYS A 166 REMARK 465 LYS A 167 REMARK 465 ALA A 168 REMARK 465 ARG A 169 REMARK 465 ALA A 170 REMARK 465 ASP A 171 REMARK 465 HIS A 172 REMARK 465 GLY A 173 REMARK 465 LEU A 356 REMARK 465 LEU A 357 REMARK 465 GLU B 146 REMARK 465 ASN B 147 REMARK 465 LEU B 148 REMARK 465 TYR B 149 REMARK 465 PHE B 150 REMARK 465 GLN B 151 REMARK 465 SER B 152 REMARK 465 ARG B 153 REMARK 465 PRO B 154 REMARK 465 ALA B 155 REMARK 465 ARG B 156 REMARK 465 GLY B 157 REMARK 465 SER B 158 REMARK 465 LEU B 159 REMARK 465 PRO B 160 REMARK 465 GLU B 161 REMARK 465 GLN B 162 REMARK 465 PRO B 163 REMARK 465 CYS B 164 REMARK 465 THR B 165 REMARK 465 LYS B 166 REMARK 465 LYS B 167 REMARK 465 ALA B 168 REMARK 465 ARG B 169 REMARK 465 ALA B 170 REMARK 465 ASP B 171 REMARK 465 HIS B 172 REMARK 465 GLY B 173 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 179 CD CE NZ REMARK 470 GLU A 266 CG CD OE1 OE2 REMARK 470 ARG A 268 CG CD NE CZ NH1 NH2 REMARK 470 THR A 354 OG1 CG2 REMARK 470 HIS A 358 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 378 CG CD CE NZ REMARK 470 LYS B 179 CG CD CE NZ REMARK 470 ARG B 268 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 353 CG OD1 OD2 REMARK 470 HIS B 355 CG ND1 CD2 CE1 NE2 REMARK 470 LEU B 356 CG CD1 CD2 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 199 -52.23 -129.43 REMARK 500 GLU A 266 97.10 -44.35 REMARK 500 ASN A 367 67.23 -151.86 REMARK 500 ARG B 189 52.52 39.55 REMARK 500 PHE B 199 -51.63 -130.38 REMARK 500 GLU B 266 98.54 -42.34 REMARK 500 ASN B 367 66.65 -152.21 REMARK 500 LYS B 397 -5.47 74.92 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 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 321 NE2 REMARK 620 2 ASP A 323 OD2 111.8 REMARK 620 3 HIS A 400 NE2 79.4 91.2 REMARK 620 4 AKG A 502 O1 159.4 87.1 109.3 REMARK 620 5 AKG A 502 O5 77.6 168.5 97.1 82.7 REMARK 620 6 HOH A 640 O 76.6 94.2 155.7 94.7 81.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 321 NE2 REMARK 620 2 ASP B 323 OD2 116.4 REMARK 620 3 HIS B 400 NE2 83.7 91.1 REMARK 620 4 AKG B 502 O5 79.1 163.7 95.8 REMARK 620 5 AKG B 502 O2 160.5 81.8 103.8 82.2 REMARK 620 6 HOH B 630 O 79.1 88.3 160.4 90.1 95.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6F4M RELATED DB: PDB REMARK 900 RELATED ID: 6F4O RELATED DB: PDB REMARK 900 RELATED ID: 6F4P RELATED DB: PDB REMARK 900 RELATED ID: 6F4Q RELATED DB: PDB REMARK 900 RELATED ID: 6F4R RELATED DB: PDB REMARK 900 RELATED ID: 6F4S RELATED DB: PDB REMARK 900 RELATED ID: 6F4T RELATED DB: PDB DBREF 6F4N A 153 416 UNP Q8N371 KDM8_HUMAN 153 416 DBREF 6F4N B 153 416 UNP Q8N371 KDM8_HUMAN 153 416 SEQADV 6F4N GLU A 146 UNP Q8N371 EXPRESSION TAG SEQADV 6F4N ASN A 147 UNP Q8N371 EXPRESSION TAG SEQADV 6F4N LEU A 148 UNP Q8N371 EXPRESSION TAG SEQADV 6F4N TYR A 149 UNP Q8N371 EXPRESSION TAG SEQADV 6F4N PHE A 150 UNP Q8N371 EXPRESSION TAG SEQADV 6F4N GLN A 151 UNP Q8N371 EXPRESSION TAG SEQADV 6F4N SER A 152 UNP Q8N371 EXPRESSION TAG SEQADV 6F4N GLU B 146 UNP Q8N371 EXPRESSION TAG SEQADV 6F4N ASN B 147 UNP Q8N371 EXPRESSION TAG SEQADV 6F4N LEU B 148 UNP Q8N371 EXPRESSION TAG SEQADV 6F4N TYR B 149 UNP Q8N371 EXPRESSION TAG SEQADV 6F4N PHE B 150 UNP Q8N371 EXPRESSION TAG SEQADV 6F4N GLN B 151 UNP Q8N371 EXPRESSION TAG SEQADV 6F4N SER B 152 UNP Q8N371 EXPRESSION TAG SEQRES 1 A 271 GLU ASN LEU TYR PHE GLN SER ARG PRO ALA ARG GLY SER SEQRES 2 A 271 LEU PRO GLU GLN PRO CYS THR LYS LYS ALA ARG ALA ASP SEQRES 3 A 271 HIS GLY LEU ILE PRO ASP VAL LYS LEU GLU LYS THR VAL SEQRES 4 A 271 PRO ARG LEU HIS ARG PRO SER LEU GLN HIS PHE ARG GLU SEQRES 5 A 271 GLN PHE LEU VAL PRO GLY ARG PRO VAL ILE LEU LYS GLY SEQRES 6 A 271 VAL ALA ASP HIS TRP PRO CYS MET GLN LYS TRP SER LEU SEQRES 7 A 271 GLU TYR ILE GLN GLU ILE ALA GLY CYS ARG THR VAL PRO SEQRES 8 A 271 VAL GLU VAL GLY SER ARG TYR THR ASP GLU GLU TRP SER SEQRES 9 A 271 GLN THR LEU MET THR VAL ASN GLU PHE ILE SER LYS TYR SEQRES 10 A 271 ILE VAL ASN GLU PRO ARG ASP VAL GLY TYR LEU ALA GLN SEQRES 11 A 271 HIS GLN LEU PHE ASP GLN ILE PRO GLU LEU LYS GLN ASP SEQRES 12 A 271 ILE SER ILE PRO ASP TYR CYS SER LEU GLY ASP GLY GLU SEQRES 13 A 271 GLU GLU GLU ILE THR ILE ASN ALA TRP PHE GLY PRO GLN SEQRES 14 A 271 GLY THR ILE SER PRO LEU HIS GLN ASP PRO GLN GLN ASN SEQRES 15 A 271 PHE LEU VAL GLN VAL MET GLY ARG LYS TYR ILE ARG LEU SEQRES 16 A 271 TYR SER PRO GLN GLU SER GLY ALA LEU TYR PRO HIS ASP SEQRES 17 A 271 THR HIS LEU LEU HIS ASN THR SER GLN VAL ASP VAL GLU SEQRES 18 A 271 ASN PRO ASP LEU GLU LYS PHE PRO LYS PHE ALA LYS ALA SEQRES 19 A 271 PRO PHE LEU SER CYS ILE LEU SER PRO GLY GLU ILE LEU SEQRES 20 A 271 PHE ILE PRO VAL LYS TYR TRP HIS TYR VAL ARG ALA LEU SEQRES 21 A 271 ASP LEU SER PHE SER VAL SER PHE TRP TRP SER SEQRES 1 B 271 GLU ASN LEU TYR PHE GLN SER ARG PRO ALA ARG GLY SER SEQRES 2 B 271 LEU PRO GLU GLN PRO CYS THR LYS LYS ALA ARG ALA ASP SEQRES 3 B 271 HIS GLY LEU ILE PRO ASP VAL LYS LEU GLU LYS THR VAL SEQRES 4 B 271 PRO ARG LEU HIS ARG PRO SER LEU GLN HIS PHE ARG GLU SEQRES 5 B 271 GLN PHE LEU VAL PRO GLY ARG PRO VAL ILE LEU LYS GLY SEQRES 6 B 271 VAL ALA ASP HIS TRP PRO CYS MET GLN LYS TRP SER LEU SEQRES 7 B 271 GLU TYR ILE GLN GLU ILE ALA GLY CYS ARG THR VAL PRO SEQRES 8 B 271 VAL GLU VAL GLY SER ARG TYR THR ASP GLU GLU TRP SER SEQRES 9 B 271 GLN THR LEU MET THR VAL ASN GLU PHE ILE SER LYS TYR SEQRES 10 B 271 ILE VAL ASN GLU PRO ARG ASP VAL GLY TYR LEU ALA GLN SEQRES 11 B 271 HIS GLN LEU PHE ASP GLN ILE PRO GLU LEU LYS GLN ASP SEQRES 12 B 271 ILE SER ILE PRO ASP TYR CYS SER LEU GLY ASP GLY GLU SEQRES 13 B 271 GLU GLU GLU ILE THR ILE ASN ALA TRP PHE GLY PRO GLN SEQRES 14 B 271 GLY THR ILE SER PRO LEU HIS GLN ASP PRO GLN GLN ASN SEQRES 15 B 271 PHE LEU VAL GLN VAL MET GLY ARG LYS TYR ILE ARG LEU SEQRES 16 B 271 TYR SER PRO GLN GLU SER GLY ALA LEU TYR PRO HIS ASP SEQRES 17 B 271 THR HIS LEU LEU HIS ASN THR SER GLN VAL ASP VAL GLU SEQRES 18 B 271 ASN PRO ASP LEU GLU LYS PHE PRO LYS PHE ALA LYS ALA SEQRES 19 B 271 PRO PHE LEU SER CYS ILE LEU SER PRO GLY GLU ILE LEU SEQRES 20 B 271 PHE ILE PRO VAL LYS TYR TRP HIS TYR VAL ARG ALA LEU SEQRES 21 B 271 ASP LEU SER PHE SER VAL SER PHE TRP TRP SER HET MN A 501 1 HET AKG A 502 10 HET MN B 501 1 HET AKG B 502 10 HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID FORMUL 3 MN 2(MN 2+) FORMUL 4 AKG 2(C5 H6 O5) FORMUL 7 HOH *189(H2 O) HELIX 1 AA1 SER A 191 PHE A 199 1 9 HELIX 2 AA2 TRP A 215 TRP A 221 1 7 HELIX 3 AA3 SER A 222 GLY A 231 1 10 HELIX 4 AA4 THR A 244 GLU A 246 5 3 HELIX 5 AA5 VAL A 255 ILE A 263 1 9 HELIX 6 AA6 GLN A 277 ILE A 282 1 6 HELIX 7 AA7 PRO A 283 ILE A 289 5 7 HELIX 8 AA8 PRO A 292 GLY A 298 5 7 HELIX 9 AA9 SER A 342 TYR A 350 5 9 HELIX 10 AB1 PHE A 373 ALA A 379 5 7 HELIX 11 AB2 SER B 191 PHE B 199 1 9 HELIX 12 AB3 TRP B 215 TRP B 221 1 7 HELIX 13 AB4 SER B 222 GLY B 231 1 10 HELIX 14 AB5 THR B 244 GLU B 246 5 3 HELIX 15 AB6 VAL B 255 ILE B 263 1 9 HELIX 16 AB7 GLN B 277 ILE B 282 1 6 HELIX 17 AB8 ILE B 282 GLN B 287 1 6 HELIX 18 AB9 PRO B 292 GLY B 298 5 7 HELIX 19 AC1 GLU B 301 ILE B 305 5 5 HELIX 20 AC2 SER B 342 TYR B 350 5 9 HELIX 21 AC3 PHE B 373 ALA B 379 5 7 SHEET 1 AA1 7 ARG A 186 HIS A 188 0 SHEET 2 AA1 7 VAL A 206 LYS A 209 1 O ILE A 207 N LEU A 187 SHEET 3 AA1 7 ILE A 391 ILE A 394 -1 O PHE A 393 N VAL A 206 SHEET 4 AA1 7 GLN A 326 MET A 333 -1 N LEU A 329 O LEU A 392 SHEET 5 AA1 7 SER A 408 TRP A 415 -1 O VAL A 411 N VAL A 330 SHEET 6 AA1 7 THR A 306 GLY A 312 -1 N GLY A 312 O SER A 408 SHEET 7 AA1 7 LEU A 273 HIS A 276 -1 N HIS A 276 O ALA A 309 SHEET 1 AA2 2 THR A 234 GLY A 240 0 SHEET 2 AA2 2 TRP A 248 THR A 254 -1 O MET A 253 N VAL A 235 SHEET 1 AA3 4 ILE A 317 HIS A 321 0 SHEET 2 AA3 4 TRP A 399 ALA A 404 -1 O VAL A 402 N SER A 318 SHEET 3 AA3 4 LYS A 336 TYR A 341 -1 N TYR A 337 O ARG A 403 SHEET 4 AA3 4 LEU A 382 LEU A 386 -1 O LEU A 382 N LEU A 340 SHEET 1 AA4 7 ARG B 186 HIS B 188 0 SHEET 2 AA4 7 VAL B 206 LYS B 209 1 O ILE B 207 N LEU B 187 SHEET 3 AA4 7 ILE B 391 ILE B 394 -1 O PHE B 393 N VAL B 206 SHEET 4 AA4 7 GLN B 326 MET B 333 -1 N LEU B 329 O LEU B 392 SHEET 5 AA4 7 SER B 408 TRP B 415 -1 O VAL B 411 N VAL B 330 SHEET 6 AA4 7 THR B 306 GLY B 312 -1 N THR B 306 O TRP B 414 SHEET 7 AA4 7 LEU B 273 HIS B 276 -1 N LEU B 273 O PHE B 311 SHEET 1 AA5 2 THR B 234 GLY B 240 0 SHEET 2 AA5 2 TRP B 248 THR B 254 -1 O MET B 253 N VAL B 235 SHEET 1 AA6 4 ILE B 317 HIS B 321 0 SHEET 2 AA6 4 TRP B 399 ALA B 404 -1 O VAL B 402 N SER B 318 SHEET 3 AA6 4 LYS B 336 TYR B 341 -1 N TYR B 337 O ARG B 403 SHEET 4 AA6 4 LEU B 382 LEU B 386 -1 O LEU B 386 N LYS B 336 SSBOND 1 CYS A 232 CYS B 232 1555 1555 2.04 LINK NE2 HIS A 321 MN MN A 501 1555 1555 2.35 LINK OD2 ASP A 323 MN MN A 501 1555 1555 2.07 LINK NE2 HIS A 400 MN MN A 501 1555 1555 2.26 LINK MN MN A 501 O1 AKG A 502 1555 1555 2.08 LINK MN MN A 501 O5 AKG A 502 1555 1555 2.16 LINK MN MN A 501 O HOH A 640 1555 1555 2.27 LINK NE2 HIS B 321 MN MN B 501 1555 1555 2.24 LINK OD2 ASP B 323 MN MN B 501 1555 1555 2.25 LINK NE2 HIS B 400 MN MN B 501 1555 1555 2.24 LINK MN MN B 501 O5 AKG B 502 1555 1555 2.25 LINK MN MN B 501 O2 AKG B 502 1555 1555 1.98 LINK MN MN B 501 O HOH B 630 1555 1555 2.46 SITE 1 AC1 5 HIS A 321 ASP A 323 HIS A 400 AKG A 502 SITE 2 AC1 5 HOH A 640 SITE 1 AC2 14 TYR A 272 TRP A 310 SER A 318 HIS A 321 SITE 2 AC2 14 ASP A 323 ASN A 327 LYS A 336 HIS A 400 SITE 3 AC2 14 VAL A 402 SER A 412 TRP A 414 MN A 501 SITE 4 AC2 14 HOH A 603 HOH A 640 SITE 1 AC3 5 HIS B 321 ASP B 323 HIS B 400 AKG B 502 SITE 2 AC3 5 HOH B 630 SITE 1 AC4 12 TYR B 272 TRP B 310 SER B 318 HIS B 321 SITE 2 AC4 12 ASP B 323 ASN B 327 LYS B 336 HIS B 400 SITE 3 AC4 12 VAL B 402 SER B 412 TRP B 414 MN B 501 CRYST1 68.002 68.002 267.898 90.00 90.00 120.00 P 32 2 1 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 0.014705 0.008490 0.000000 0.00000 SCALE2 0.000000 0.016980 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003733 0.00000