HEADER HYDROLASE 12-OCT-18 6IJY TITLE CRYSTAL STRUCTURE OF HUMAN MTH1(G2K/C87A/C104S MUTANT) IN COMPLEX WITH TITLE 2 8-OXO-DGTP DETERMINED USING A CRYSTAL OBTAINED UNDER MICROGRAVITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 2-HYDROXY-DATP DIPHOSPHATASE,8-OXO-DGTPASE,NUCLEOSIDE COMPND 5 DIPHOSPHATE-LINKED MOIETY X MOTIF 1,NUDIX MOTIF 1; COMPND 6 EC: 3.6.1.55,3.6.1.56; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NUDT1, MTH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ALPHA-BETA-ALPHA SANDWICH, HYDROLASE, DNA DAMAGE, DNA REPAIR, DNA KEYWDS 2 REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR T.NAKAMURA,Y.YAMAGATA REVDAT 2 27-MAR-24 6IJY 1 JRNL LINK REVDAT 1 20-FEB-19 6IJY 0 JRNL AUTH T.NAKAMURA,K.HIRATA,K.FUJIMIYA,M.CHIRIFU,T.ARIMORI,T.TAMADA, JRNL AUTH 2 S.IKEMIZU,Y.YAMAGATA JRNL TITL X-RAY STRUCTURE ANALYSIS OF HUMAN OXIDIZED NUCLEOTIDE JRNL TITL 2 HYDROLASE MTH1 USING CRYSTALS OBTAINED UNDER MICROGRAVITY. JRNL REF INT. J. MICROGRAVITY SCI. V. 36 2019 JRNL REF 2 APPL. JRNL REFN ESSN 2188-9783 JRNL DOI 10.15011//JASMA.36.360103 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.WAZ,T.NAKAMURA,K.HIRATA,Y.KOGA-OGAWA,M.CHIRIFU,T.ARIMORI, REMARK 1 AUTH 2 T.TAMADA,S.IKEMIZU,Y.NAKABEPPU,Y.YAMAGATA REMARK 1 TITL STRUCTURAL AND KINETIC STUDIES OF THE HUMAN NUDIX HYDROLASE REMARK 1 TITL 2 MTH1 REVEAL THE MECHANISM FOR ITS BROAD SUBSTRATE REMARK 1 TITL 3 SPECIFICITY. REMARK 1 REF J. BIOL. CHEM. V. 292 2785 2017 REMARK 1 REFN ESSN 1083-351X REMARK 1 PMID 28035004 REMARK 1 DOI 10.1074/JBC.M116.749713 REMARK 1 REFERENCE 2 REMARK 1 AUTH Y.KOGA,M.INAZATO,T.NAKAMURA,C.HASHIKAWA,M.CHIRIFU,A.MICHI, REMARK 1 AUTH 2 T.YAMASHITA,S.TOMA,A.KUNIYASU,S.IKEMIZU,Y.NAKABEPPU, REMARK 1 AUTH 3 Y.YAMAGATA REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF HUMAN MTH1 REMARK 1 TITL 2 WITH A HOMOGENEOUS N-TERMINUS. REMARK 1 REF ACTA CRYSTALLOGR. SECT. F V. 69 45 2013 REMARK 1 REF 2 STRUCT. BIOL. CRYST. COMMUN. REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 23295485 REMARK 1 DOI 10.1107/S1744309112048002 REMARK 2 REMARK 2 RESOLUTION. 1.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 1.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 131001 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 6595 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 38.0216 - 3.2300 0.99 4410 232 0.1649 0.1847 REMARK 3 2 3.2300 - 2.5639 1.00 4270 245 0.1561 0.2011 REMARK 3 3 2.5639 - 2.2399 1.00 4255 216 0.1416 0.1605 REMARK 3 4 2.2399 - 2.0351 1.00 4228 214 0.1273 0.1386 REMARK 3 5 2.0351 - 1.8892 1.00 4163 244 0.1221 0.1378 REMARK 3 6 1.8892 - 1.7779 1.00 4171 222 0.1190 0.1381 REMARK 3 7 1.7779 - 1.6888 1.00 4190 202 0.1187 0.1467 REMARK 3 8 1.6888 - 1.6153 1.00 4147 238 0.1154 0.1435 REMARK 3 9 1.6153 - 1.5531 1.00 4194 208 0.1108 0.1465 REMARK 3 10 1.5531 - 1.4995 1.00 4137 234 0.1072 0.1398 REMARK 3 11 1.4995 - 1.4526 1.00 4147 217 0.1074 0.1389 REMARK 3 12 1.4526 - 1.4111 1.00 4164 200 0.1057 0.1290 REMARK 3 13 1.4111 - 1.3740 1.00 4131 197 0.1063 0.1390 REMARK 3 14 1.3740 - 1.3404 1.00 4139 226 0.1055 0.1279 REMARK 3 15 1.3404 - 1.3100 1.00 4166 212 0.1066 0.1395 REMARK 3 16 1.3100 - 1.2821 1.00 4134 223 0.1078 0.1371 REMARK 3 17 1.2821 - 1.2564 1.00 4127 207 0.1072 0.1389 REMARK 3 18 1.2564 - 1.2327 1.00 4144 193 0.1082 0.1440 REMARK 3 19 1.2327 - 1.2107 1.00 4099 232 0.1062 0.1307 REMARK 3 20 1.2107 - 1.1902 1.00 4152 218 0.1098 0.1255 REMARK 3 21 1.1902 - 1.1710 1.00 4092 206 0.1091 0.1320 REMARK 3 22 1.1710 - 1.1530 1.00 4161 223 0.1131 0.1264 REMARK 3 23 1.1530 - 1.1360 1.00 4046 247 0.1152 0.1427 REMARK 3 24 1.1360 - 1.1200 1.00 4086 215 0.1187 0.1470 REMARK 3 25 1.1200 - 1.1049 1.00 4130 224 0.1269 0.1552 REMARK 3 26 1.1049 - 1.0905 1.00 4114 218 0.1298 0.1470 REMARK 3 27 1.0905 - 1.0769 1.00 4148 232 0.1364 0.1533 REMARK 3 28 1.0769 - 1.0639 1.00 4049 223 0.1530 0.1838 REMARK 3 29 1.0639 - 1.0515 1.00 4085 235 0.1811 0.1988 REMARK 3 30 1.0515 - 1.0397 0.96 3927 192 0.2498 0.2967 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.480 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) : 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 : 0.008 3150 REMARK 3 ANGLE : 1.376 4326 REMARK 3 CHIRALITY : 0.081 439 REMARK 3 PLANARITY : 0.009 561 REMARK 3 DIHEDRAL : 16.574 1193 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 6IJY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1300009328. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-17 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 : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 131109 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.040 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 65.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.06 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.90000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, CACODYLATE, SODIUM REMARK 280 CHLORIDE, GLYCEROL, COUNTER-DIFFUSION, TEMPERATURE 293K 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 22.74600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.96800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.04950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.96800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.74600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.04950 REMARK 290 SMTRY3 4 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 TOTAL BURIED SURFACE AREA: 240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 GLN A 92 20.00 -143.86 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 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 36 O REMARK 620 2 GLU A 56 OE2 86.3 REMARK 620 3 8DG A 201 O1B 99.9 92.4 REMARK 620 4 8DG A 201 O2A 108.7 165.0 84.3 REMARK 620 5 HOH A 395 O 89.7 85.9 170.2 94.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 204 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 52 OE1 REMARK 620 2 GLU A 56 OE2 92.8 REMARK 620 3 8DG A 201 O1B 111.7 89.3 REMARK 620 4 HOH A 303 O 85.0 116.3 149.3 REMARK 620 5 HOH A 311 O 83.5 163.6 77.4 79.4 REMARK 620 6 HOH A 314 O 155.2 108.3 82.0 74.3 79.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 203 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 113 O REMARK 620 2 MET A 116 O 91.4 REMARK 620 3 HOH A 388 O 76.4 86.1 REMARK 620 4 HOH B 411 O 84.6 166.7 80.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 119 OD1 REMARK 620 2 ASP B 119 OD2 47.1 REMARK 620 3 ASP B 120 OD1 87.1 81.1 REMARK 620 4 8DG B 201 O6 109.8 129.9 148.5 REMARK 620 5 HOH B 343 O 163.4 132.9 77.0 82.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8DG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8DG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 202 DBREF 6IJY A 1 156 UNP P36639 8ODP_HUMAN 42 197 DBREF 6IJY B 1 156 UNP P36639 8ODP_HUMAN 42 197 SEQADV 6IJY LYS A 2 UNP P36639 GLY 43 ENGINEERED MUTATION SEQADV 6IJY ALA A 87 UNP P36639 CYS 128 ENGINEERED MUTATION SEQADV 6IJY SER A 104 UNP P36639 CYS 145 ENGINEERED MUTATION SEQADV 6IJY LYS B 2 UNP P36639 GLY 43 ENGINEERED MUTATION SEQADV 6IJY ALA B 87 UNP P36639 CYS 128 ENGINEERED MUTATION SEQADV 6IJY SER B 104 UNP P36639 CYS 145 ENGINEERED MUTATION SEQRES 1 A 156 MET LYS ALA SER ARG LEU TYR THR LEU VAL LEU VAL LEU SEQRES 2 A 156 GLN PRO GLN ARG VAL LEU LEU GLY MET LYS LYS ARG GLY SEQRES 3 A 156 PHE GLY ALA GLY ARG TRP ASN GLY PHE GLY GLY LYS VAL SEQRES 4 A 156 GLN GLU GLY GLU THR ILE GLU ASP GLY ALA ARG ARG GLU SEQRES 5 A 156 LEU GLN GLU GLU SER GLY LEU THR VAL ASP ALA LEU HIS SEQRES 6 A 156 LYS VAL GLY GLN ILE VAL PHE GLU PHE VAL GLY GLU PRO SEQRES 7 A 156 GLU LEU MET ASP VAL HIS VAL PHE ALA THR ASP SER ILE SEQRES 8 A 156 GLN GLY THR PRO VAL GLU SER ASP GLU MET ARG PRO SER SEQRES 9 A 156 TRP PHE GLN LEU ASP GLN ILE PRO PHE LYS ASP MET TRP SEQRES 10 A 156 PRO ASP ASP SER TYR TRP PHE PRO LEU LEU LEU GLN LYS SEQRES 11 A 156 LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN GLY GLN ASP SEQRES 12 A 156 THR ILE LEU ASP TYR THR LEU ARG GLU VAL ASP THR VAL SEQRES 1 B 156 MET LYS ALA SER ARG LEU TYR THR LEU VAL LEU VAL LEU SEQRES 2 B 156 GLN PRO GLN ARG VAL LEU LEU GLY MET LYS LYS ARG GLY SEQRES 3 B 156 PHE GLY ALA GLY ARG TRP ASN GLY PHE GLY GLY LYS VAL SEQRES 4 B 156 GLN GLU GLY GLU THR ILE GLU ASP GLY ALA ARG ARG GLU SEQRES 5 B 156 LEU GLN GLU GLU SER GLY LEU THR VAL ASP ALA LEU HIS SEQRES 6 B 156 LYS VAL GLY GLN ILE VAL PHE GLU PHE VAL GLY GLU PRO SEQRES 7 B 156 GLU LEU MET ASP VAL HIS VAL PHE ALA THR ASP SER ILE SEQRES 8 B 156 GLN GLY THR PRO VAL GLU SER ASP GLU MET ARG PRO SER SEQRES 9 B 156 TRP PHE GLN LEU ASP GLN ILE PRO PHE LYS ASP MET TRP SEQRES 10 B 156 PRO ASP ASP SER TYR TRP PHE PRO LEU LEU LEU GLN LYS SEQRES 11 B 156 LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN GLY GLN ASP SEQRES 12 B 156 THR ILE LEU ASP TYR THR LEU ARG GLU VAL ASP THR VAL HET 8DG A 201 32 HET NA A 202 1 HET NA A 203 1 HET NA A 204 1 HET GOL A 205 6 HET GOL A 206 6 HET 8DG B 201 64 HET NA B 202 1 HETNAM 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 8DG 2(C10 H16 N5 O14 P3) FORMUL 4 NA 4(NA 1+) FORMUL 7 GOL 2(C3 H8 O3) FORMUL 11 HOH *324(H2 O) HELIX 1 AA1 THR A 44 GLY A 58 1 15 HELIX 2 AA2 PRO A 112 MET A 116 5 5 HELIX 3 AA3 TRP A 117 PRO A 118 5 2 HELIX 4 AA4 ASP A 119 GLN A 129 1 11 HELIX 5 AA5 THR B 44 GLY B 58 1 15 HELIX 6 AA6 PRO B 112 MET B 116 5 5 HELIX 7 AA7 TRP B 117 PRO B 118 5 2 HELIX 8 AA8 ASP B 119 GLN B 129 1 11 SHEET 1 AA1 3 TRP A 32 ASN A 33 0 SHEET 2 AA1 3 ARG A 17 LYS A 23 -1 N GLY A 21 O ASN A 33 SHEET 3 AA1 3 MET A 101 GLN A 107 -1 O SER A 104 N LEU A 20 SHEET 1 AA2 7 TRP A 32 ASN A 33 0 SHEET 2 AA2 7 ARG A 17 LYS A 23 -1 N GLY A 21 O ASN A 33 SHEET 3 AA2 7 SER A 4 LEU A 13 -1 N VAL A 12 O LEU A 19 SHEET 4 AA2 7 LEU A 80 THR A 88 1 O PHE A 86 N LEU A 9 SHEET 5 AA2 7 HIS A 65 PHE A 74 -1 N ILE A 70 O VAL A 83 SHEET 6 AA2 7 PHE A 133 GLN A 140 1 O PHE A 139 N GLU A 73 SHEET 7 AA2 7 THR A 144 GLU A 152 -1 O ASP A 147 N LYS A 138 SHEET 1 AA3 2 THR A 60 VAL A 61 0 SHEET 2 AA3 2 ILE A 91 GLN A 92 -1 O GLN A 92 N THR A 60 SHEET 1 AA4 4 TRP B 32 ASN B 33 0 SHEET 2 AA4 4 ARG B 17 LYS B 23 -1 N GLY B 21 O ASN B 33 SHEET 3 AA4 4 SER B 4 LEU B 13 -1 N VAL B 12 O LEU B 19 SHEET 4 AA4 4 MET B 101 GLN B 107 0 SHEET 1 AA5 7 PHE B 35 LYS B 38 0 SHEET 2 AA5 7 SER B 4 LEU B 13 -1 N VAL B 10 O PHE B 35 SHEET 3 AA5 7 ARG B 17 LYS B 23 -1 O LEU B 19 N VAL B 12 SHEET 4 AA5 7 LEU B 80 THR B 88 0 SHEET 5 AA5 7 LEU B 64 PHE B 74 -1 N ILE B 70 O VAL B 83 SHEET 6 AA5 7 PHE B 133 GLN B 140 1 O PHE B 137 N GLU B 73 SHEET 7 AA5 7 THR B 144 GLU B 152 -1 O ASP B 147 N LYS B 138 LINK O GLY A 36 NA NA A 202 1555 1555 2.29 LINK OE1 GLU A 52 NA NA A 204 1555 1555 2.29 LINK OE2 GLU A 56 NA NA A 202 1555 1555 2.31 LINK OE2 GLU A 56 NA NA A 204 1555 1555 2.42 LINK O PHE A 113 NA NA A 203 1555 1555 2.19 LINK O MET A 116 NA NA A 203 1555 1555 2.74 LINK O1B 8DG A 201 NA NA A 202 1555 1555 2.36 LINK O2A 8DG A 201 NA NA A 202 1555 1555 2.31 LINK O1B 8DG A 201 NA NA A 204 1555 1555 2.38 LINK NA NA A 202 O HOH A 395 1555 1555 2.34 LINK NA NA A 203 O HOH A 388 1555 1555 2.70 LINK NA NA A 203 O HOH B 411 1555 3544 2.77 LINK NA NA A 204 O HOH A 303 1555 1555 2.50 LINK NA NA A 204 O HOH A 311 1555 1555 2.87 LINK NA NA A 204 O HOH A 314 1555 1555 2.37 LINK OD1 ASP B 119 NA B NA B 202 1555 1555 3.00 LINK OD2 ASP B 119 NA B NA B 202 1555 1555 2.35 LINK OD1 ASP B 120 NA B NA B 202 1555 1555 2.34 LINK O6 B8DG B 201 NA B NA B 202 1555 1555 2.38 LINK NA B NA B 202 O BHOH B 343 1555 1555 2.07 SITE 1 AC1 29 TYR A 7 THR A 8 LEU A 9 LYS A 23 SITE 2 AC1 29 ARG A 25 PHE A 27 ASN A 33 GLY A 36 SITE 3 AC1 29 GLY A 37 LYS A 38 GLU A 56 PHE A 72 SITE 4 AC1 29 MET A 81 TRP A 117 ASP A 119 ASP A 120 SITE 5 AC1 29 TRP A 123 NA A 202 NA A 204 HOH A 311 SITE 6 AC1 29 HOH A 314 HOH A 326 HOH A 331 HOH A 336 SITE 7 AC1 29 HOH A 363 HOH A 381 HOH A 390 HOH A 405 SITE 8 AC1 29 LYS B 130 SITE 1 AC2 5 GLY A 36 GLU A 56 8DG A 201 NA A 204 SITE 2 AC2 5 HOH A 395 SITE 1 AC3 4 PHE A 113 MET A 116 HOH A 388 HOH B 411 SITE 1 AC4 7 GLU A 52 GLU A 56 8DG A 201 NA A 202 SITE 2 AC4 7 HOH A 303 HOH A 311 HOH A 314 SITE 1 AC5 7 LYS A 2 VAL A 75 GLY A 76 SER A 121 SITE 2 AC5 7 TYR A 122 HOH A 456 HOH B 320 SITE 1 AC6 8 HOH A 426 LYS B 2 GLU B 73 VAL B 75 SITE 2 AC6 8 GLY B 76 GLU B 77 TYR B 122 HOH B 452 SITE 1 AC7 28 LYS A 130 HOH A 309 HOH A 320 HOH A 325 SITE 2 AC7 28 HOH A 385 TYR B 7 THR B 8 LEU B 9 SITE 3 AC7 28 ASN B 33 GLY B 36 GLY B 37 LYS B 38 SITE 4 AC7 28 GLU B 52 GLU B 56 PHE B 72 PHE B 74 SITE 5 AC7 28 MET B 81 TRP B 117 ASP B 119 ASP B 120 SITE 6 AC7 28 TRP B 123 PHE B 139 NA B 202 HOH B 313 SITE 7 AC7 28 HOH B 316 HOH B 342 HOH B 343 HOH B 344 SITE 1 AC8 5 TRP B 117 ASP B 119 ASP B 120 8DG B 201 SITE 2 AC8 5 HOH B 343 CRYST1 45.492 48.099 123.936 90.00 90.00 90.00 P 21 21 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 0.021982 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008069 0.00000