HEADER HYDROLASE 26-AUG-16 5T3P TITLE CRYSTAL STRUCTURE OF HUMAN PEROXISOMAL COENZYME A DIPHOSPHATASE NUDT7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOMAL COENZYME A DIPHOSPHATASE NUDT7; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 7,NUDIX MOTIF COMPND 5 7; COMPND 6 EC: 3.6.1.-; COMPND 7 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: NUDT7; 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: PNIC28-BSA4 KEYWDS COA HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.SRIKANNATHASAN,C.A.NUNEZ,C.TALLANT,P.SIEJKA,S.MATHEA,J.KOPEC, AUTHOR 2 J.M.ELKINS,N.BURGESS-BROWN,C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA, AUTHOR 3 F.VON DELFT,K.HUBER REVDAT 3 17-JAN-24 5T3P 1 REMARK REVDAT 2 07-FEB-18 5T3P 1 REMARK REVDAT 1 13-SEP-17 5T3P 0 JRNL AUTH V.SRIKANNATHASAN JRNL TITL CRYSTAL STRUCTURE OF HUMAN PEROXISOMAL COENZYME A JRNL TITL 2 DIPHOSPHATASE NUDT7 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1682 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 52595 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2680 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 56.8873 - 5.4154 1.00 2781 155 0.1601 0.2059 REMARK 3 2 5.4154 - 4.2988 1.00 2679 161 0.1314 0.1655 REMARK 3 3 4.2988 - 3.7555 1.00 2644 149 0.1461 0.1915 REMARK 3 4 3.7555 - 3.4122 1.00 2650 139 0.1668 0.2203 REMARK 3 5 3.4122 - 3.1677 1.00 2638 126 0.1922 0.2690 REMARK 3 6 3.1677 - 2.9809 1.00 2641 144 0.2117 0.2378 REMARK 3 7 2.9809 - 2.8316 1.00 2649 115 0.2100 0.2750 REMARK 3 8 2.8316 - 2.7084 1.00 2598 132 0.2068 0.2182 REMARK 3 9 2.7084 - 2.6041 1.00 2644 157 0.2114 0.2960 REMARK 3 10 2.6041 - 2.5143 1.00 2606 133 0.2044 0.2710 REMARK 3 11 2.5143 - 2.4356 1.00 2629 129 0.2127 0.2494 REMARK 3 12 2.4356 - 2.3660 1.00 2555 168 0.1966 0.2781 REMARK 3 13 2.3660 - 2.3037 1.00 2612 126 0.2030 0.2683 REMARK 3 14 2.3037 - 2.2475 1.00 2589 153 0.2093 0.2796 REMARK 3 15 2.2475 - 2.1964 1.00 2591 159 0.2036 0.2539 REMARK 3 16 2.1964 - 2.1497 1.00 2582 147 0.2187 0.2744 REMARK 3 17 2.1497 - 2.1067 1.00 2621 122 0.2257 0.2698 REMARK 3 18 2.1067 - 2.0669 1.00 2573 154 0.2518 0.3141 REMARK 3 19 2.0669 - 2.0300 1.00 2633 111 0.2725 0.3377 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.34 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 : 0.009 5371 REMARK 3 ANGLE : 1.069 7292 REMARK 3 CHIRALITY : 0.050 832 REMARK 3 PLANARITY : 0.006 947 REMARK 3 DIHEDRAL : 13.214 1964 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 44.6932 56.9100 40.8533 REMARK 3 T TENSOR REMARK 3 T11: 0.3053 T22: 0.2650 REMARK 3 T33: 0.2443 T12: 0.0277 REMARK 3 T13: 0.0461 T23: 0.0100 REMARK 3 L TENSOR REMARK 3 L11: 0.6452 L22: 0.7882 REMARK 3 L33: 0.6360 L12: -0.0008 REMARK 3 L13: 0.2351 L23: -0.1716 REMARK 3 S TENSOR REMARK 3 S11: 0.0516 S12: 0.0726 S13: -0.0102 REMARK 3 S21: -0.2178 S22: -0.0367 S23: -0.0952 REMARK 3 S31: 0.0820 S32: 0.0855 S33: -0.0107 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 5T3P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000223520. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 R CDTE 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52595 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 56.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.50 REMARK 200 R MERGE (I) : 0.07920 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 9.80 REMARK 200 R MERGE FOR SHELL (I) : 1.38200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.710 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1NQZ REMARK 200 REMARK 200 REMARK: HEXAGONAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8M SODIUM PHOSPHATE MONOBASIC, 0.8M REMARK 280 POTTASSIUM PHOSPHATE DIBASIC, 0.1M HEPES PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 36.06667 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 72.13333 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 72.13333 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 36.06667 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 HOH A 501 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 SER A 1 REMARK 465 MET A 2 REMARK 465 SER A 3 REMARK 465 ARG A 4 REMARK 465 LEU A 5 REMARK 465 GLY A 6 REMARK 465 LEU A 7 REMARK 465 PRO A 8 REMARK 465 GLU A 9 REMARK 465 GLU A 10 REMARK 465 PRO A 11 REMARK 465 VAL A 12 REMARK 465 ARG A 13 REMARK 465 LYS A 233 REMARK 465 LYS A 234 REMARK 465 ALA A 235 REMARK 465 THR A 236 REMARK 465 SER B 1 REMARK 465 MET B 2 REMARK 465 SER B 3 REMARK 465 ARG B 4 REMARK 465 LEU B 5 REMARK 465 GLY B 6 REMARK 465 LEU B 7 REMARK 465 PRO B 8 REMARK 465 GLU B 9 REMARK 465 GLU B 10 REMARK 465 PRO B 11 REMARK 465 VAL B 12 REMARK 465 ARG B 13 REMARK 465 LYS B 234 REMARK 465 ALA B 235 REMARK 465 THR B 236 REMARK 465 SER C 1 REMARK 465 MET C 2 REMARK 465 SER C 3 REMARK 465 ARG C 4 REMARK 465 LEU C 5 REMARK 465 GLY C 6 REMARK 465 LEU C 7 REMARK 465 PRO C 8 REMARK 465 GLU C 9 REMARK 465 GLU C 10 REMARK 465 PRO C 11 REMARK 465 VAL C 12 REMARK 465 ARG C 13 REMARK 465 ALA C 235 REMARK 465 THR C 236 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 134 CG CD OE1 NE2 REMARK 470 HIS A 162 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 166 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 167 CG CD1 CD2 REMARK 470 GLU A 226 CG CD OE1 OE2 REMARK 470 LYS A 230 CG CD CE NZ REMARK 470 ASN B 14 CG OD1 ND2 REMARK 470 ARG B 166 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 170 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 208 CG CD CE NZ REMARK 470 LYS B 230 CG CD CE NZ REMARK 470 LYS C 26 CG CD CE NZ REMARK 470 LEU C 167 CG CD1 CD2 REMARK 470 LYS C 233 CG CD CE NZ REMARK 470 LYS C 234 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 NZ LYS B 64 O HOH B 401 2.16 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 O1 EDO C 303 O HOH C 430 4556 2.09 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 166 95.44 -164.94 REMARK 500 HIS A 169 131.85 66.91 REMARK 500 THR A 210 33.15 -87.67 REMARK 500 ASP A 219 51.39 -151.34 REMARK 500 SER B 15 -73.41 21.77 REMARK 500 LYS B 32 -26.52 -38.87 REMARK 500 GLU B 51 42.97 39.22 REMARK 500 ASP B 219 57.12 -160.74 REMARK 500 PRO C 37 46.48 -75.22 REMARK 500 THR C 210 30.76 -85.35 REMARK 500 ASP C 219 59.75 -158.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 513 DISTANCE = 5.86 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 303 DBREF 5T3P A 2 236 UNP P0C024 NUDT7_HUMAN 1 235 DBREF 5T3P B 2 236 UNP P0C024 NUDT7_HUMAN 1 235 DBREF 5T3P C 2 236 UNP P0C024 NUDT7_HUMAN 1 235 SEQADV 5T3P SER A 1 UNP P0C024 EXPRESSION TAG SEQADV 5T3P SER B 1 UNP P0C024 EXPRESSION TAG SEQADV 5T3P SER C 1 UNP P0C024 EXPRESSION TAG SEQRES 1 A 236 SER MET SER ARG LEU GLY LEU PRO GLU GLU PRO VAL ARG SEQRES 2 A 236 ASN SER LEU LEU ASP ASP ALA LYS ALA ARG LEU ARG LYS SEQRES 3 A 236 TYR ASP ILE GLY GLY LYS TYR SER HIS LEU PRO TYR ASN SEQRES 4 A 236 LYS TYR SER VAL LEU LEU PRO LEU VAL ALA LYS GLU GLY SEQRES 5 A 236 LYS LEU HIS LEU LEU PHE THR VAL ARG SER GLU LYS LEU SEQRES 6 A 236 ARG ARG ALA PRO GLY GLU VAL CYS PHE PRO GLY GLY LYS SEQRES 7 A 236 ARG ASP PRO THR ASP MET ASP ASP ALA ALA THR ALA LEU SEQRES 8 A 236 ARG GLU ALA GLN GLU GLU VAL GLY LEU ARG PRO HIS GLN SEQRES 9 A 236 VAL GLU VAL VAL CYS CYS LEU VAL PRO CYS LEU ILE ASP SEQRES 10 A 236 THR ASP THR LEU ILE THR PRO PHE VAL GLY LEU ILE ASP SEQRES 11 A 236 HIS ASN PHE GLN ALA GLN PRO ASN PRO ALA GLU VAL LYS SEQRES 12 A 236 ASP VAL PHE LEU VAL PRO LEU ALA TYR PHE LEU HIS PRO SEQRES 13 A 236 GLN VAL HIS ASP GLN HIS TYR VAL THR ARG LEU GLY HIS SEQRES 14 A 236 ARG PHE ILE ASN HIS ILE PHE GLU TYR THR ASN PRO GLU SEQRES 15 A 236 ASP GLY VAL THR TYR GLN ILE LYS GLY MET THR ALA ASN SEQRES 16 A 236 LEU ALA VAL LEU VAL ALA PHE ILE ILE LEU GLU LYS LYS SEQRES 17 A 236 PRO THR PHE GLU VAL GLN PHE ASN LEU ASN ASP VAL LEU SEQRES 18 A 236 ALA SER SER GLU GLU LEU PHE LEU LYS VAL HIS LYS LYS SEQRES 19 A 236 ALA THR SEQRES 1 B 236 SER MET SER ARG LEU GLY LEU PRO GLU GLU PRO VAL ARG SEQRES 2 B 236 ASN SER LEU LEU ASP ASP ALA LYS ALA ARG LEU ARG LYS SEQRES 3 B 236 TYR ASP ILE GLY GLY LYS TYR SER HIS LEU PRO TYR ASN SEQRES 4 B 236 LYS TYR SER VAL LEU LEU PRO LEU VAL ALA LYS GLU GLY SEQRES 5 B 236 LYS LEU HIS LEU LEU PHE THR VAL ARG SER GLU LYS LEU SEQRES 6 B 236 ARG ARG ALA PRO GLY GLU VAL CYS PHE PRO GLY GLY LYS SEQRES 7 B 236 ARG ASP PRO THR ASP MET ASP ASP ALA ALA THR ALA LEU SEQRES 8 B 236 ARG GLU ALA GLN GLU GLU VAL GLY LEU ARG PRO HIS GLN SEQRES 9 B 236 VAL GLU VAL VAL CYS CYS LEU VAL PRO CYS LEU ILE ASP SEQRES 10 B 236 THR ASP THR LEU ILE THR PRO PHE VAL GLY LEU ILE ASP SEQRES 11 B 236 HIS ASN PHE GLN ALA GLN PRO ASN PRO ALA GLU VAL LYS SEQRES 12 B 236 ASP VAL PHE LEU VAL PRO LEU ALA TYR PHE LEU HIS PRO SEQRES 13 B 236 GLN VAL HIS ASP GLN HIS TYR VAL THR ARG LEU GLY HIS SEQRES 14 B 236 ARG PHE ILE ASN HIS ILE PHE GLU TYR THR ASN PRO GLU SEQRES 15 B 236 ASP GLY VAL THR TYR GLN ILE LYS GLY MET THR ALA ASN SEQRES 16 B 236 LEU ALA VAL LEU VAL ALA PHE ILE ILE LEU GLU LYS LYS SEQRES 17 B 236 PRO THR PHE GLU VAL GLN PHE ASN LEU ASN ASP VAL LEU SEQRES 18 B 236 ALA SER SER GLU GLU LEU PHE LEU LYS VAL HIS LYS LYS SEQRES 19 B 236 ALA THR SEQRES 1 C 236 SER MET SER ARG LEU GLY LEU PRO GLU GLU PRO VAL ARG SEQRES 2 C 236 ASN SER LEU LEU ASP ASP ALA LYS ALA ARG LEU ARG LYS SEQRES 3 C 236 TYR ASP ILE GLY GLY LYS TYR SER HIS LEU PRO TYR ASN SEQRES 4 C 236 LYS TYR SER VAL LEU LEU PRO LEU VAL ALA LYS GLU GLY SEQRES 5 C 236 LYS LEU HIS LEU LEU PHE THR VAL ARG SER GLU LYS LEU SEQRES 6 C 236 ARG ARG ALA PRO GLY GLU VAL CYS PHE PRO GLY GLY LYS SEQRES 7 C 236 ARG ASP PRO THR ASP MET ASP ASP ALA ALA THR ALA LEU SEQRES 8 C 236 ARG GLU ALA GLN GLU GLU VAL GLY LEU ARG PRO HIS GLN SEQRES 9 C 236 VAL GLU VAL VAL CYS CYS LEU VAL PRO CYS LEU ILE ASP SEQRES 10 C 236 THR ASP THR LEU ILE THR PRO PHE VAL GLY LEU ILE ASP SEQRES 11 C 236 HIS ASN PHE GLN ALA GLN PRO ASN PRO ALA GLU VAL LYS SEQRES 12 C 236 ASP VAL PHE LEU VAL PRO LEU ALA TYR PHE LEU HIS PRO SEQRES 13 C 236 GLN VAL HIS ASP GLN HIS TYR VAL THR ARG LEU GLY HIS SEQRES 14 C 236 ARG PHE ILE ASN HIS ILE PHE GLU TYR THR ASN PRO GLU SEQRES 15 C 236 ASP GLY VAL THR TYR GLN ILE LYS GLY MET THR ALA ASN SEQRES 16 C 236 LEU ALA VAL LEU VAL ALA PHE ILE ILE LEU GLU LYS LYS SEQRES 17 C 236 PRO THR PHE GLU VAL GLN PHE ASN LEU ASN ASP VAL LEU SEQRES 18 C 236 ALA SER SER GLU GLU LEU PHE LEU LYS VAL HIS LYS LYS SEQRES 19 C 236 ALA THR HET EDO A 301 4 HET EDO A 302 4 HET EDO A 303 4 HET EDO A 304 4 HET EDO B 301 4 HET EDO B 302 4 HET EDO B 303 4 HET EDO C 301 4 HET EDO C 302 4 HET EDO C 303 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 EDO 10(C2 H6 O2) FORMUL 14 HOH *314(H2 O) HELIX 1 AA1 SER A 15 ARG A 25 1 11 HELIX 2 AA2 LYS A 26 ASP A 28 5 3 HELIX 3 AA3 ASP A 85 GLY A 99 1 15 HELIX 4 AA4 ARG A 101 HIS A 103 5 3 HELIX 5 AA5 ALA A 151 LEU A 154 5 4 HELIX 6 AA6 GLY A 191 GLU A 206 1 16 HELIX 7 AA7 ASP A 219 LYS A 230 1 12 HELIX 8 AA8 SER B 15 LYS B 26 1 12 HELIX 9 AA9 TYR B 27 ASP B 28 5 2 HELIX 10 AB1 ILE B 29 SER B 34 5 6 HELIX 11 AB2 ASP B 85 GLY B 99 1 15 HELIX 12 AB3 ARG B 101 HIS B 103 5 3 HELIX 13 AB4 ALA B 151 LEU B 154 5 4 HELIX 14 AB5 GLY B 191 GLU B 206 1 16 HELIX 15 AB6 ASP B 219 LYS B 233 1 15 HELIX 16 AB7 SER C 15 LYS C 26 1 12 HELIX 17 AB8 ASP C 85 GLY C 99 1 15 HELIX 18 AB9 ARG C 101 HIS C 103 5 3 HELIX 19 AC1 ALA C 151 LEU C 154 5 4 HELIX 20 AC2 GLY C 191 GLU C 206 1 16 HELIX 21 AC3 ASP C 219 LYS C 234 1 16 SHEET 1 A 4 PRO A 75 LYS A 78 0 SHEET 2 A 4 ASN A 39 LEU A 47 -1 SHEET 3 A 4 THR A 120 ILE A 129 1 SHEET 4 A 4 VAL A 105 CYS A 110 -1 SHEET 1 B 3 PRO A 46 LYS A 50 0 SHEET 2 B 3 LYS A 53 ARG A 61 -1 SHEET 3 B 3 VAL A 142 PRO A 149 -1 SHEET 1 C 3 VAL A 158 THR A 165 0 SHEET 2 C 3 ARG A 170 THR A 179 -1 SHEET 3 C 3 THR A 186 LYS A 190 -1 SHEET 1 D 4 GLY B 76 LYS B 78 0 SHEET 2 D 4 ASN B 39 LEU B 47 -1 SHEET 3 D 4 THR B 120 ILE B 129 1 SHEET 4 D 4 VAL B 105 CYS B 110 -1 SHEET 1 E 3 PRO B 46 LYS B 50 0 SHEET 2 E 3 LYS B 53 ARG B 61 -1 SHEET 3 E 3 VAL B 142 PRO B 149 -1 SHEET 1 F 3 HIS B 159 ARG B 166 0 SHEET 2 F 3 HIS B 169 THR B 179 -1 SHEET 3 F 3 THR B 186 LYS B 190 -1 SHEET 1 G 2 CYS B 114 ASP B 117 0 SHEET 2 G 2 THR B 120 ILE B 122 -1 SHEET 1 H 4 GLY C 76 LYS C 78 0 SHEET 2 H 4 ASN C 39 LEU C 47 -1 SHEET 3 H 4 THR C 120 ILE C 129 1 SHEET 4 H 4 VAL C 105 CYS C 110 -1 SHEET 1 I 3 PRO C 46 LYS C 50 0 SHEET 2 I 3 LYS C 53 ARG C 61 -1 SHEET 3 I 3 VAL C 142 PRO C 149 -1 SHEET 1 J 3 HIS C 159 ARG C 166 0 SHEET 2 J 3 HIS C 169 THR C 179 -1 SHEET 3 J 3 THR C 186 LYS C 190 -1 SHEET 1 K 2 CYS C 114 ASP C 117 0 SHEET 2 K 2 THR C 120 ILE C 122 -1 CISPEP 1 ARG A 166 LEU A 167 0 -5.74 CISPEP 2 LEU A 167 GLY A 168 0 -11.19 SITE 1 AC1 4 GLN A 95 GLU A 96 GLN A 136 ASN A 138 SITE 1 AC2 4 ASP A 28 VAL A 107 VAL A 108 CYS A 110 SITE 1 AC3 5 TYR A 41 ARG A 66 ARG A 67 EDO A 304 SITE 2 AC3 5 LYS B 64 SITE 1 AC4 4 TYR A 41 ARG A 66 LYS A 78 EDO A 303 SITE 1 AC5 6 ASP B 28 VAL B 107 VAL B 108 CYS B 109 SITE 2 AC5 6 CYS B 110 MET C 84 SITE 1 AC6 5 LYS A 64 TYR B 41 ARG B 66 ARG B 67 SITE 2 AC6 5 EDO B 303 SITE 1 AC7 4 TYR B 41 ARG B 66 LYS B 78 EDO B 302 SITE 1 AC8 2 TYR C 187 GLN C 188 SITE 1 AC9 6 ASN C 39 TYR C 41 ARG C 66 ARG C 67 SITE 2 AC9 6 LYS C 78 EDO C 303 SITE 1 AD1 7 TYR C 41 LYS C 64 ARG C 66 ARG C 67 SITE 2 AD1 7 EDO C 302 HOH C 401 HOH C 430 CRYST1 113.730 113.730 108.200 90.00 90.00 120.00 P 31 2 1 18 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 0.008793 0.005076 0.000000 0.00000 SCALE2 0.000000 0.010153 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009242 0.00000