PDB Short entry for 6PCL HEADER HYDROLASE 17-JUN-19 6PCL TITLE CRYSTAL STRUCTURE OF HUMAN DIPHOSPHOINOSITOL POLYPHOSPHATE TITLE 2 PHOSPHOHYDROLASE 1 IN COMPLEX WITH 5-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 6PCL 1 LINK REVDAT 2 13-MAY-20 6PCL 1 JRNL REVDAT 1 29-APR-20 6PCL 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. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.890 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 3 NUMBER OF REFLECTIONS : 38468 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.161 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1935 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 27.6308 - 2.7905 0.99 4286 193 0.1571 0.1734 REMARK 3 2 2.7905 - 2.2152 1.00 4094 236 0.1318 0.1491 REMARK 3 3 2.2152 - 1.9353 1.00 4085 211 0.1194 0.1437 REMARK 3 4 1.9353 - 1.7584 0.98 3973 223 0.1237 0.1431 REMARK 3 5 1.7584 - 1.6324 0.98 3963 200 0.1264 0.1479 REMARK 3 6 1.6324 - 1.5361 0.96 3898 220 0.1232 0.1466 REMARK 3 7 1.5361 - 1.4592 0.92 3678 187 0.1309 0.1597 REMARK 3 8 1.4592 - 1.3957 0.83 3364 191 0.1481 0.1655 REMARK 3 9 1.3957 - 1.3420 0.74 2975 158 0.1575 0.1999 REMARK 3 10 1.3420 - 1.2957 0.55 2217 116 0.1780 0.1919 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 : 0.46 REMARK 3 B_SOL : 60.25 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.840 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.860 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) : 7.29760 REMARK 3 B22 (A**2) : -4.39900 REMARK 3 B33 (A**2) : -2.89860 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 : 0.011 1238 REMARK 3 ANGLE : 1.374 1708 REMARK 3 CHIRALITY : 0.087 171 REMARK 3 PLANARITY : 0.007 214 REMARK 3 DIHEDRAL : 13.849 514 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 8:33) REMARK 3 ORIGIN FOR THE GROUP (A): 4.3849 4.7700 17.4701 REMARK 3 T TENSOR REMARK 3 T11: 0.0859 T22: 0.1211 REMARK 3 T33: 0.1132 T12: 0.0079 REMARK 3 T13: -0.0212 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.2330 L22: 0.7787 REMARK 3 L33: 0.6883 L12: -0.0245 REMARK 3 L13: 0.2477 L23: 0.0670 REMARK 3 S TENSOR REMARK 3 S11: -0.0175 S12: 0.0388 S13: 0.0243 REMARK 3 S21: 0.1231 S22: -0.0075 S23: 0.0388 REMARK 3 S31: -0.0203 S32: 0.0292 S33: -0.0077 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 34:73) REMARK 3 ORIGIN FOR THE GROUP (A): 8.4375 9.7502 16.7565 REMARK 3 T TENSOR REMARK 3 T11: 0.0934 T22: 0.1189 REMARK 3 T33: 0.1244 T12: 0.0045 REMARK 3 T13: -0.0092 T23: -0.0052 REMARK 3 L TENSOR REMARK 3 L11: 0.7408 L22: 0.9978 REMARK 3 L33: 1.2212 L12: -0.4358 REMARK 3 L13: 0.3554 L23: 0.0386 REMARK 3 S TENSOR REMARK 3 S11: -0.0111 S12: -0.0062 S13: 0.1053 REMARK 3 S21: 0.0562 S22: 0.0374 S23: -0.1807 REMARK 3 S31: -0.0856 S32: 0.1690 S33: -0.0162 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 74:117) REMARK 3 ORIGIN FOR THE GROUP (A): 5.2210 10.1667 15.5825 REMARK 3 T TENSOR REMARK 3 T11: 0.0695 T22: 0.1022 REMARK 3 T33: 0.1392 T12: -0.0051 REMARK 3 T13: -0.0013 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.2301 L22: 1.2035 REMARK 3 L33: 0.9271 L12: -0.4038 REMARK 3 L13: 0.0792 L23: 0.0599 REMARK 3 S TENSOR REMARK 3 S11: -0.0178 S12: -0.0125 S13: 0.0894 REMARK 3 S21: 0.0114 S22: 0.0328 S23: -0.1230 REMARK 3 S31: -0.0437 S32: 0.1091 S33: -0.0157 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 118:142) REMARK 3 ORIGIN FOR THE GROUP (A): 3.2313 2.7307 4.3790 REMARK 3 T TENSOR REMARK 3 T11: 0.1322 T22: 0.1451 REMARK 3 T33: 0.0997 T12: 0.0203 REMARK 3 T13: -0.0078 T23: -0.0052 REMARK 3 L TENSOR REMARK 3 L11: 0.7423 L22: 0.9229 REMARK 3 L33: 0.3526 L12: -0.6257 REMARK 3 L13: -0.0376 L23: 0.2069 REMARK 3 S TENSOR REMARK 3 S11: 0.0831 S12: 0.1333 S13: -0.1014 REMARK 3 S21: -0.2299 S22: -0.0735 S23: 0.0816 REMARK 3 S31: -0.0491 S32: -0.0214 S33: 0.0054 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 6PCL 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_1000242331. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-19 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-BM 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 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40069 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 27.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 58.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 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) : 0.36500 REMARK 200 <I/SIGMA(I)> 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 (%): 50.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 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 22.78000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.17900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.78800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.17900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.78000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.78800 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 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 GLN A 8 CG CD OE1 NE2 REMARK 470 ARG A 41 CG CD NE CZ NH1 NH2 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 HOH A 315 O HOH A 400 2.10 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. = 3.6 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 GLU A 56 13.55 59.39 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 83.2 REMARK 620 3 I7P A 201 O25 91.2 169.1 REMARK 620 4 I7P A 201 O44 166.7 93.6 94.0 REMARK 620 5 I7P A 201 O65 100.0 82.3 89.5 92.3 REMARK 620 6 HOH A 314 O 81.2 89.4 99.0 85.9 171.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 66 OE1 REMARK 620 2 GLU A 70 OE2 110.1 REMARK 620 3 I7P A 201 O65 106.1 84.9 REMARK 620 4 HOH A 355 O 107.5 117.7 128.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 66 OE2 REMARK 620 2 I7P A 201 O55 105.6 REMARK 620 3 HOH A 350 O 99.3 107.8 REMARK 620 4 HOH A 358 O 108.6 122.4 110.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue I7P 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 MG A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 206 DBREF 6PCL 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 I7P A 201 40 HET MG A 202 1 HET MG A 203 1 HET MG A 204 1 HET CL A 205 1 HET CL A 206 1 HETNAM I7P (1R,2R,3S,4S,5R,6S)-2,3,4,5,6-PENTAKIS(PHOSPHONOOXY) HETNAM 2 I7P CYCLOHEXYL TRIHYDROGEN DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETSYN I7P 1D-MYO-INOSITOL 5-DIPHOSPHATE 1,2,3,4,6- HETSYN 2 I7P PENTAKISPHOSPHATE FORMUL 2 I7P C6 H19 O27 P7 FORMUL 3 MG 3(MG 2+) FORMUL 6 CL 2(CL 1-) FORMUL 8 HOH *160(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 PHE A 120 N VAL A 34 LINK O GLY A 50 MG MG A 202 1555 1555 2.17 LINK OE1 GLU A 66 MG MG A 203 1555 1555 2.05 LINK OE2 GLU A 66 MG MG A 204 1555 1555 2.05 LINK OE2 GLU A 70 MG MG A 202 1555 1555 2.06 LINK OE2 GLU A 70 MG MG A 203 1555 1555 2.04 LINK O25 I7P A 201 MG MG A 202 1555 1555 2.10 LINK O44 I7P A 201 MG MG A 202 1555 1555 2.01 LINK O65 I7P A 201 MG MG A 202 1555 1555 2.03 LINK O65 I7P A 201 MG MG A 203 1555 1555 1.96 LINK O55 I7P A 201 MG MG A 204 1555 1555 1.92 LINK MG MG A 202 O HOH A 314 1555 1555 2.12 LINK MG MG A 203 O HOH A 355 1555 1555 1.77 LINK MG MG A 204 O HOH A 350 1555 1555 1.95 LINK MG MG A 204 O HOH A 358 1555 1555 1.91 SITE 1 AC1 29 ARG A 10 LYS A 18 ARG A 20 SER A 39 SITE 2 AC1 29 SER A 40 ILE A 47 GLY A 50 GLY A 51 SITE 3 AC1 29 GLY A 52 GLU A 66 GLU A 70 ARG A 89 SITE 4 AC1 29 HIS A 91 ARG A 115 LYS A 133 MG A 202 SITE 5 AC1 29 MG A 203 MG A 204 HOH A 302 HOH A 314 SITE 6 AC1 29 HOH A 325 HOH A 332 HOH A 336 HOH A 346 SITE 7 AC1 29 HOH A 351 HOH A 357 HOH A 359 HOH A 360 SITE 8 AC1 29 HOH A 363 SITE 1 AC2 5 GLY A 50 GLU A 70 I7P A 201 MG A 203 SITE 2 AC2 5 HOH A 314 SITE 1 AC3 7 GLY A 50 GLU A 66 GLU A 70 I7P A 201 SITE 2 AC3 7 MG A 202 MG A 204 HOH A 355 SITE 1 AC4 6 GLY A 52 GLU A 66 I7P A 201 MG A 203 SITE 2 AC4 6 HOH A 350 HOH A 358 SITE 1 AC5 3 ASN A 86 HIS A 91 GLN A 136 SITE 1 AC6 6 SER A 28 SER A 30 GLU A 31 GLU A 32 SITE 2 AC6 6 GLU A 33 HOH A 443 CRYST1 45.560 59.576 62.358 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 0.021949 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016785 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016036 0.00000