HEADER OXIDOREDUCTASE 23-NOV-18 6I9M TITLE JMJC DOMAIN-CONTAINING PROTEIN 5 (JMJD5) IN COMPLEX WITH MN AND R-2- TITLE 2 HYDROXYGLUTARATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: JMJC DOMAIN-CONTAINING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: JUMONJI DOMAIN-CONTAINING PROTEIN 5,LYSINE-SPECIFIC COMPND 5 DEMETHYLASE 8; COMPND 6 EC: 1.14.11.27,3.4.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: CATALYTIC DOMAIN (RESIDUES 183-416) 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_PLASMID: PLASMID 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 31-JAN-24 6I9M 1 REMARK REVDAT 2 21-DEC-22 6I9M 1 JRNL LINK REVDAT 1 04-DEC-19 6I9M 0 JRNL AUTH M.S.ISLAM,M.MARKOULIDES,R.CHOWDHURY,C.J.SCHOFIELD JRNL TITL STRUCTURAL ANALYSIS OF THE 2-OXOGLUTARATE BINDING SITE OF JRNL TITL 2 THE CIRCADIAN RHYTHM LINKED OXYGENASE JMJD5. JRNL REF SCI REP V. 12 20680 2022 JRNL REFN ESSN 2045-2322 JRNL PMID 36450832 JRNL DOI 10.1038/S41598-022-24154-0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.E.WILKINS,M.S.ISLAM,J.M.GANNON,S.MARKOLOVIC,R.J.HOPKINSON, REMARK 1 AUTH 2 W.GE,C.J.SCHOFIELD,R.CHOWDHURY REMARK 1 TITL JMJD5 IS A HUMAN ARGINYL C-3 HYDROXYLASE. REMARK 1 REF NAT COMMUN V. 9 1180 2018 REMARK 1 REFN ESSN 2041-1723 REMARK 1 PMID 29563586 REMARK 1 DOI 10.1038/S41467-018-03410-W REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 30541 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1500 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 41.7628 - 3.6685 1.00 2826 141 0.1631 0.1978 REMARK 3 2 3.6685 - 2.9120 1.00 2697 131 0.1451 0.1540 REMARK 3 3 2.9120 - 2.5439 1.00 2666 143 0.1425 0.1837 REMARK 3 4 2.5439 - 2.3114 1.00 2641 141 0.1378 0.1570 REMARK 3 5 2.3114 - 2.1457 1.00 2611 138 0.1402 0.1729 REMARK 3 6 2.1457 - 2.0192 1.00 2648 132 0.1389 0.1716 REMARK 3 7 2.0192 - 1.9181 1.00 2604 138 0.1372 0.1836 REMARK 3 8 1.9181 - 1.8346 1.00 2608 137 0.1523 0.1723 REMARK 3 9 1.8346 - 1.7640 1.00 2606 130 0.1555 0.2074 REMARK 3 10 1.7640 - 1.7031 1.00 2609 128 0.1773 0.2249 REMARK 3 11 1.7031 - 1.6498 0.97 2525 141 0.2041 0.2494 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 : 0.42 REMARK 3 B_SOL : 51.80 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.00 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 : 0.018 2079 REMARK 3 ANGLE : 1.400 2861 REMARK 3 CHIRALITY : 0.113 302 REMARK 3 PLANARITY : 0.011 373 REMARK 3 DIHEDRAL : 11.128 1273 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: NULL REMARK 4 REMARK 4 6I9M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1200013060. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-15 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 : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98000 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 706E REMARK 200 DATA SCALING SOFTWARE : HKL-2000 706E REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30597 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 41.749 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.78800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.180 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 (%): 47.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 15.0 % PEG3350, REMARK 280 0.002 M MNCL2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 24.78550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.71850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.33700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.71850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.78550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.33700 REMARK 290 SMTRY3 4 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 161 REMARK 465 HIS A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 SER A 168 REMARK 465 SER A 169 REMARK 465 GLY A 170 REMARK 465 VAL A 171 REMARK 465 ASP A 172 REMARK 465 LEU A 173 REMARK 465 GLY A 174 REMARK 465 THR A 175 REMARK 465 GLU A 176 REMARK 465 ASN A 177 REMARK 465 LEU A 178 REMARK 465 TYR A 179 REMARK 465 PHE A 180 REMARK 465 GLN A 181 REMARK 465 SER A 241 REMARK 465 ARG A 242 REMARK 465 TYR A 243 REMARK 465 THR A 244 REMARK 465 ASP A 245 REMARK 465 GLU A 246 REMARK 465 GLU A 247 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 GLN A 193 CD OE1 NE2 REMARK 470 GLN A 219 CD OE1 NE2 REMARK 470 TRP A 248 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 248 CZ3 CH2 REMARK 470 LYS A 261 CD CE NZ REMARK 470 GLU A 284 CG CD OE1 OE2 REMARK 470 ASP A 353 CG OD1 OD2 REMARK 470 LEU A 356 CG CD1 CD2 REMARK 470 LYS A 378 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 HE21 GLN A 275 O HOH A 603 1.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 204 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES 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 ARG A 189 63.77 34.29 REMARK 500 PHE A 199 -51.50 -128.84 REMARK 500 PHE A 199 -51.50 -137.92 REMARK 500 ILE A 263 -58.26 -123.54 REMARK 500 ILE A 263 -63.27 -120.72 REMARK 500 GLU A 266 103.07 -46.61 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 111.5 REMARK 620 3 HIS A 400 NE2 83.2 83.6 REMARK 620 4 2HG A 502 O3 83.2 163.5 91.2 REMARK 620 5 2HG A 502 O1 156.6 91.7 103.2 74.3 REMARK 620 6 HOH A 666 O 85.5 88.0 162.3 101.0 92.5 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 2HG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 506 DBREF 6I9M A 183 416 UNP Q8N371 KDM8_HUMAN 183 416 SEQADV 6I9M MET A 161 UNP Q8N371 INITIATING METHIONINE SEQADV 6I9M HIS A 162 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M HIS A 163 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M HIS A 164 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M HIS A 165 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M HIS A 166 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M HIS A 167 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M SER A 168 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M SER A 169 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M GLY A 170 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M VAL A 171 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M ASP A 172 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M LEU A 173 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M GLY A 174 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M THR A 175 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M GLU A 176 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M ASN A 177 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M LEU A 178 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M TYR A 179 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M PHE A 180 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M GLN A 181 UNP Q8N371 EXPRESSION TAG SEQADV 6I9M SER A 182 UNP Q8N371 EXPRESSION TAG SEQRES 1 A 256 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 256 GLY THR GLU ASN LEU TYR PHE GLN SER THR VAL PRO ARG SEQRES 3 A 256 LEU HIS ARG PRO SER LEU GLN HIS PHE ARG GLU GLN PHE SEQRES 4 A 256 LEU VAL PRO GLY ARG PRO VAL ILE LEU LYS GLY VAL ALA SEQRES 5 A 256 ASP HIS TRP PRO CYS MET GLN LYS TRP SER LEU GLU TYR SEQRES 6 A 256 ILE GLN GLU ILE ALA GLY CYS ARG THR VAL PRO VAL GLU SEQRES 7 A 256 VAL GLY SER ARG TYR THR ASP GLU GLU TRP SER GLN THR SEQRES 8 A 256 LEU MET THR VAL ASN GLU PHE ILE SER LYS TYR ILE VAL SEQRES 9 A 256 ASN GLU PRO ARG ASP VAL GLY TYR LEU ALA GLN HIS GLN SEQRES 10 A 256 LEU PHE ASP GLN ILE PRO GLU LEU LYS GLN ASP ILE SER SEQRES 11 A 256 ILE PRO ASP TYR CYS SER LEU GLY ASP GLY GLU GLU GLU SEQRES 12 A 256 GLU ILE THR ILE ASN ALA TRP PHE GLY PRO GLN GLY THR SEQRES 13 A 256 ILE SER PRO LEU HIS GLN ASP PRO GLN GLN ASN PHE LEU SEQRES 14 A 256 VAL GLN VAL MET GLY ARG LYS TYR ILE ARG LEU TYR SER SEQRES 15 A 256 PRO GLN GLU SER GLY ALA LEU TYR PRO HIS ASP THR HIS SEQRES 16 A 256 LEU LEU HIS ASN THR SER GLN VAL ASP VAL GLU ASN PRO SEQRES 17 A 256 ASP LEU GLU LYS PHE PRO LYS PHE ALA LYS ALA PRO PHE SEQRES 18 A 256 LEU SER CYS ILE LEU SER PRO GLY GLU ILE LEU PHE ILE SEQRES 19 A 256 PRO VAL LYS TYR TRP HIS TYR VAL ARG ALA LEU ASP LEU SEQRES 20 A 256 SER PHE SER VAL SER PHE TRP TRP SER HET MN A 501 1 HET 2HG A 502 16 HET TRS A 503 20 HET GOL A 504 14 HET GOL A 505 14 HET GOL A 506 14 HETNAM MN MANGANESE (II) ION HETNAM 2HG (2R)-2-HYDROXYPENTANEDIOIC ACID HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM GOL GLYCEROL HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MN MN 2+ FORMUL 3 2HG C5 H8 O5 FORMUL 4 TRS C4 H12 N O3 1+ FORMUL 5 GOL 3(C3 H8 O3) FORMUL 8 HOH *193(H2 O) HELIX 1 AA1 SER A 191 PHE A 199 1 9 HELIX 2 AA2 PRO A 216 TRP A 221 1 6 HELIX 3 AA3 SER A 222 GLY A 231 1 10 HELIX 4 AA4 VAL A 255 ILE A 263 1 9 HELIX 5 AA5 GLN A 277 ILE A 282 1 6 HELIX 6 AA6 PRO A 283 ILE A 289 5 7 HELIX 7 AA7 PRO A 292 GLY A 298 5 7 HELIX 8 AA8 GLU A 301 ILE A 305 5 5 HELIX 9 AA9 SER A 342 TYR A 350 5 9 HELIX 10 AB1 PHE A 373 ALA A 379 5 7 SHEET 1 AA1 9 ARG A 186 HIS A 188 0 SHEET 2 AA1 9 VAL A 206 LYS A 209 1 O LYS A 209 N LEU A 187 SHEET 3 AA1 9 ILE A 391 ILE A 394 -1 O PHE A 393 N VAL A 206 SHEET 4 AA1 9 GLN A 326 MET A 333 -1 N LEU A 329 O LEU A 392 SHEET 5 AA1 9 SER A 408 TRP A 415 -1 O VAL A 411 N VAL A 330 SHEET 6 AA1 9 THR A 306 GLY A 312 -1 N GLY A 312 O SER A 408 SHEET 7 AA1 9 GLY A 271 HIS A 276 -1 N HIS A 276 O ALA A 309 SHEET 8 AA1 9 THR A 234 VAL A 239 -1 N GLU A 238 O TYR A 272 SHEET 9 AA1 9 SER A 249 THR A 254 -1 O SER A 249 N VAL A 239 SHEET 1 AA2 4 ILE A 317 HIS A 321 0 SHEET 2 AA2 4 TRP A 399 ALA A 404 -1 O VAL A 402 N SER A 318 SHEET 3 AA2 4 LYS A 336 TYR A 341 -1 N TYR A 337 O ARG A 403 SHEET 4 AA2 4 LEU A 382 LEU A 386 -1 O LEU A 386 N LYS A 336 LINK NE2 HIS A 321 MN MN A 501 1555 1555 2.24 LINK OD2 ASP A 323 MN MN A 501 1555 1555 2.16 LINK NE2 HIS A 400 MN MN A 501 1555 1555 2.33 LINK MN MN A 501 O3 2HG A 502 1555 1555 2.20 LINK MN MN A 501 O1 2HG A 502 1555 1555 2.19 LINK MN MN A 501 O HOH A 666 1555 1555 2.22 SITE 1 AC1 5 HIS A 321 ASP A 323 HIS A 400 2HG A 502 SITE 2 AC1 5 HOH A 666 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 LEU A 329 LYS A 336 SITE 3 AC2 14 HIS A 400 VAL A 402 SER A 412 TRP A 414 SITE 4 AC2 14 MN A 501 HOH A 697 SITE 1 AC3 10 LEU A 200 VAL A 201 GLY A 203 GLN A 326 SITE 2 AC3 10 TYR A 350 LYS A 372 PHE A 373 VAL A 396 SITE 3 AC3 10 HOH A 605 HOH A 624 SITE 1 AC4 5 ARG A 189 GLU A 266 ASP A 293 TYR A 294 SITE 2 AC4 5 HOH A 655 SITE 1 AC5 6 GLN A 275 SER A 318 HIS A 321 ASN A 359 SITE 2 AC5 6 HOH A 666 HOH A 683 SITE 1 AC6 5 HIS A 352 SER A 361 VAL A 363 ASP A 364 SITE 2 AC6 5 HOH A 613 CRYST1 49.571 64.674 77.437 90.00 90.00 90.00 P 21 21 21 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 0.020173 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015462 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012914 0.00000