HEADER HYDROLASE 17-JUN-19 6PCK TITLE CRYSTAL STRUCTURE OF HUMAN DIPHOSPHOINOSITOL POLYPHOSPHATE TITLE 2 PHOSPHOHYDROLASE 1 IN COMPLEX WITH 1-IP7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-148; COMPND 5 SYNONYM: DIPP-1,DIADENOSINE 5',5'''-P1,P6-HEXAPHOSPHATE HYDROLASE 1, COMPND 6 NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 3,NUDIX MOTIF 3; COMPND 7 EC: 3.6.1.52,3.6.1.-; COMPND 8 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: NUDT3, DIPP, DIPP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INOSITOL PYROPHOSPHATE, INOSITOL PHOSPHATE, KINASE, PHOSPHATASE, KEYWDS 2 PPIP5K, CELL POLARITY, OSMOTIC RESPONSE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.E.DOLLINS,J.NEUBAUER,J.DONG,J.D.YORK REVDAT 3 11-OCT-23 6PCK 1 REMARK REVDAT 2 13-MAY-20 6PCK 1 JRNL REVDAT 1 29-APR-20 6PCK 0 JRNL AUTH D.E.DOLLINS,W.BAI,P.C.FRIDY,J.C.OTTO,J.L.NEUBAUER, JRNL AUTH 2 S.G.GATTIS,K.P.M.MEHTA,J.D.YORK JRNL TITL VIP1 IS A KINASE AND PYROPHOSPHATASE SWITCH THAT REGULATES JRNL TITL 2 INOSITOL DIPHOSPHATE SIGNALING. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 9356 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 32303658 JRNL DOI 10.1073/PNAS.1908875117 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.4_6) 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.890 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 47532 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2366 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 27.3845 - 2.5847 0.99 5178 253 0.1659 0.1899 REMARK 3 2 2.5847 - 2.0518 1.00 4995 272 0.1310 0.1461 REMARK 3 3 2.0518 - 1.7925 0.99 4927 263 0.1355 0.1386 REMARK 3 4 1.7925 - 1.6286 0.98 4873 247 0.1387 0.1414 REMARK 3 5 1.6286 - 1.5119 0.98 4837 268 0.1441 0.1654 REMARK 3 6 1.5119 - 1.4227 0.97 4760 248 0.1493 0.1744 REMARK 3 7 1.4227 - 1.3515 0.92 4490 234 0.1570 0.1662 REMARK 3 8 1.3515 - 1.2927 0.84 4080 232 0.1650 0.1892 REMARK 3 9 1.2927 - 1.2429 0.76 3757 180 0.1727 0.1981 REMARK 3 10 1.2429 - 1.2000 0.67 3269 169 0.1773 0.2099 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 : 0.50 REMARK 3 B_SOL : 66.21 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.700 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.480 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) : 10.08560 REMARK 3 B22 (A**2) : -6.00630 REMARK 3 B33 (A**2) : -4.07930 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 : 0.022 1221 REMARK 3 ANGLE : 1.898 1681 REMARK 3 CHIRALITY : 0.100 170 REMARK 3 PLANARITY : 0.008 213 REMARK 3 DIHEDRAL : 14.602 515 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 9:33 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.4349 4.0745 17.4167 REMARK 3 T TENSOR REMARK 3 T11: 0.0363 T22: 0.1338 REMARK 3 T33: 0.1224 T12: 0.0095 REMARK 3 T13: -0.0108 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.3651 L22: 0.5568 REMARK 3 L33: 0.8055 L12: 0.1599 REMARK 3 L13: 0.3812 L23: 0.3133 REMARK 3 S TENSOR REMARK 3 S11: -0.0731 S12: 0.0683 S13: 0.1252 REMARK 3 S21: 0.1550 S22: -0.0395 S23: 0.0225 REMARK 3 S31: -0.0335 S32: 0.0356 S33: 0.0853 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 34:73 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.7649 9.0869 16.7150 REMARK 3 T TENSOR REMARK 3 T11: 0.0489 T22: 0.1330 REMARK 3 T33: 0.1378 T12: 0.0059 REMARK 3 T13: -0.0053 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 1.0249 L22: 1.0289 REMARK 3 L33: 0.4392 L12: -0.4917 REMARK 3 L13: 0.2796 L23: -0.1549 REMARK 3 S TENSOR REMARK 3 S11: -0.0311 S12: -0.0034 S13: 0.1222 REMARK 3 S21: 0.1017 S22: -0.0047 S23: -0.1614 REMARK 3 S31: -0.0490 S32: 0.1527 S33: 0.0077 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 74:117 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.8490 9.0197 15.5244 REMARK 3 T TENSOR REMARK 3 T11: 0.0178 T22: 0.1106 REMARK 3 T33: 0.1474 T12: -0.0068 REMARK 3 T13: -0.0093 T23: -0.0023 REMARK 3 L TENSOR REMARK 3 L11: 0.6398 L22: 1.1992 REMARK 3 L33: 0.9689 L12: -0.6064 REMARK 3 L13: -0.0416 L23: -0.1721 REMARK 3 S TENSOR REMARK 3 S11: -0.0289 S12: -0.0231 S13: 0.1116 REMARK 3 S21: 0.0586 S22: 0.0239 S23: -0.0937 REMARK 3 S31: -0.0099 S32: 0.0848 S33: 0.0032 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 118:142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.6108 2.7479 4.3316 REMARK 3 T TENSOR REMARK 3 T11: 0.0845 T22: 0.1604 REMARK 3 T33: 0.1236 T12: 0.0211 REMARK 3 T13: -0.0051 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 0.6709 L22: 0.5240 REMARK 3 L33: 0.3405 L12: -0.4959 REMARK 3 L13: -0.1580 L23: 0.2388 REMARK 3 S TENSOR REMARK 3 S11: 0.0903 S12: 0.1424 S13: -0.0825 REMARK 3 S21: -0.2693 S22: -0.0935 S23: 0.0703 REMARK 3 S31: 0.0977 S32: -0.0314 S33: 0.0343 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 6PCK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1000242329. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51322 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 27.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 70.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37500 REMARK 200 FOR SHELL : NULL 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: 2Q9P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12 - 18% PEG 8000, 150 - 300 MM LISO4, REMARK 280 0.1 M SODIUM ACETATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290.15K 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 23.20550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.27800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.30600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.27800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.20550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.30600 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 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 1 REMARK 465 MET A 2 REMARK 465 LYS A 3 REMARK 465 LEU A 4 REMARK 465 LYS A 5 REMARK 465 SER A 6 REMARK 465 ASN A 7 REMARK 465 GLN A 8 REMARK 465 LEU A 143 REMARK 465 ARG A 144 REMARK 465 GLN A 145 REMARK 465 GLY A 146 REMARK 465 TYR A 147 REMARK 465 SER A 148 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 GLU A 29 CG CD OE1 OE2 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 GLU A 105 O HOH A 301 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 68 CB CYS A 68 SG -0.109 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 20 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 65 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 117 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 TYR A 139 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES 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 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 50 O REMARK 620 2 GLU A 70 OE2 81.0 REMARK 620 3 O81 A 201 O46 167.8 95.9 REMARK 620 4 O81 A 201 O21 88.3 165.5 96.5 REMARK 620 5 O81 A 201 O47 98.6 81.4 92.6 90.5 REMARK 620 6 HOH A 313 O 80.7 88.4 87.4 99.6 169.8 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 O81 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 204 DBREF 6PCK A 1 148 UNP O95989 NUDT3_HUMAN 1 148 SEQRES 1 A 148 MET MET LYS LEU LYS SER ASN GLN THR ARG THR TYR ASP SEQRES 2 A 148 GLY ASP GLY TYR LYS LYS ARG ALA ALA CYS LEU CYS PHE SEQRES 3 A 148 ARG SER GLU SER GLU GLU GLU VAL LEU LEU VAL SER SER SEQRES 4 A 148 SER ARG HIS PRO ASP ARG TRP ILE VAL PRO GLY GLY GLY SEQRES 5 A 148 MET GLU PRO GLU GLU GLU PRO SER VAL ALA ALA VAL ARG SEQRES 6 A 148 GLU VAL CYS GLU GLU ALA GLY VAL LYS GLY THR LEU GLY SEQRES 7 A 148 ARG LEU VAL GLY ILE PHE GLU ASN GLN GLU ARG LYS HIS SEQRES 8 A 148 ARG THR TYR VAL TYR VAL LEU ILE VAL THR GLU VAL LEU SEQRES 9 A 148 GLU ASP TRP GLU ASP SER VAL ASN ILE GLY ARG LYS ARG SEQRES 10 A 148 GLU TRP PHE LYS ILE GLU ASP ALA ILE LYS VAL LEU GLN SEQRES 11 A 148 TYR HIS LYS PRO VAL GLN ALA SER TYR PHE GLU THR LEU SEQRES 12 A 148 ARG GLN GLY TYR SER HET O81 A 201 40 HET MG A 202 1 HET CL A 203 1 HET CL A 204 1 HETNAM O81 (1S,2R,3R,4S,5S,6R)-2,3,4,5,6-PENTAKIS(PHOSPHONOOXY) HETNAM 2 O81 CYCLOHEXYL TRIHYDROGEN DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION FORMUL 2 O81 C6 H19 O27 P7 FORMUL 3 MG MG 2+ FORMUL 4 CL 2(CL 1-) FORMUL 6 HOH *220(H2 O) HELIX 1 AA1 GLU A 58 GLY A 72 1 15 HELIX 2 AA2 TRP A 107 GLY A 114 1 8 HELIX 3 AA3 ILE A 122 GLN A 130 1 9 HELIX 4 AA4 LYS A 133 TYR A 139 1 7 SHEET 1 AA1 4 GLY A 50 GLY A 52 0 SHEET 2 AA1 4 LYS A 18 PHE A 26 -1 N ALA A 21 O GLY A 51 SHEET 3 AA1 4 HIS A 91 VAL A 103 1 O ARG A 92 N LYS A 18 SHEET 4 AA1 4 VAL A 73 ASN A 86 -1 N GLY A 78 O VAL A 97 SHEET 1 AA2 3 TRP A 46 ILE A 47 0 SHEET 2 AA2 3 GLU A 33 SER A 38 -1 N VAL A 37 O ILE A 47 SHEET 3 AA2 3 ARG A 117 LYS A 121 -1 O GLU A 118 N LEU A 36 LINK O GLY A 50 MG MG A 202 1555 1555 2.15 LINK OE2 GLU A 70 MG MG A 202 1555 1555 1.99 LINK O46 O81 A 201 MG MG A 202 1555 1555 1.97 LINK O21 O81 A 201 MG MG A 202 1555 1555 1.89 LINK O47 O81 A 201 MG MG A 202 1555 1555 2.02 LINK MG MG A 202 O HOH A 313 1555 1555 2.16 SITE 1 AC1 32 ARG A 10 LYS A 18 ARG A 20 SER A 39 SITE 2 AC1 32 SER A 40 ARG A 41 ILE A 47 GLY A 50 SITE 3 AC1 32 GLY A 51 GLY A 52 GLU A 66 GLU A 70 SITE 4 AC1 32 ARG A 89 HIS A 91 ARG A 115 LYS A 133 SITE 5 AC1 32 MG A 202 HOH A 309 HOH A 313 HOH A 314 SITE 6 AC1 32 HOH A 315 HOH A 318 HOH A 339 HOH A 350 SITE 7 AC1 32 HOH A 353 HOH A 354 HOH A 364 HOH A 367 SITE 8 AC1 32 HOH A 380 HOH A 384 HOH A 396 HOH A 444 SITE 1 AC2 5 GLY A 50 GLY A 51 GLU A 70 O81 A 201 SITE 2 AC2 5 HOH A 313 SITE 1 AC3 3 ASN A 86 HIS A 91 GLN A 136 SITE 1 AC4 7 ARG A 27 SER A 28 SER A 30 GLU A 31 SITE 2 AC4 7 GLU A 32 GLU A 33 HOH A 480 CRYST1 46.411 56.612 62.556 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 0.021547 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017664 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015986 0.00000