HEADER HYDROLASE 30-OCT-25 9T4D TITLE HUMAN DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 1 (DIPP1) R41A TITLE 2 MUTANT IN COMPLEX WITH 5-(PP)-IP5 (5-IP7) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIPP-1,DIADENOSINE HEXAPHOSPHATE HYDROLASE,AP6A HYDROLASE, COMPND 5 ENDOPOLYPHOSPHATASE,NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 3, COMPND 6 NUDIX MOTIF 3,M7GPPPN-MRNA HYDROLASE,M7GPPPX DIPHOSPHATASE; COMPND 7 EC: 3.6.1.52,3.6.1.61,3.6.1.10,3.6.1.62,3.6.1.59; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: DELETION OF THE LAST 24 C-TERMINAL RESIDUES (149-172), COMPND 11 THE FIRST THREE AMINO ACIDS (GHM) REMAIN AS RESIDUAL RESIDUES AFTER COMPND 12 REMOVAL OF THE EXPRESSION TAG. 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 BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: STAR KEYWDS INOSITOL METABOLISM, PHOSPHATASE, NUDIX HYDROLASES, DIPP1, IP7, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.CASAS-FLOREZ,M.A.MARQUEZ-MONINO,B.GONZALEZ REVDAT 1 10-JUN-26 9T4D 0 JRNL AUTH D.CASAS-FLOREZ,H.WHITFIELD,J.M.PEREZ-CANADILLAS, JRNL AUTH 2 B.MONTERROSO,A.M.RILEY,M.A.MARQUEZ-MONINO,M.L.SHIPTON, JRNL AUTH 3 J.SANZ-APARICIO,C.A.BREARLEY,B.V.L.POTTER,B.GONZALEZ JRNL TITL THE DIPP1 FAMILY BINDS IP 8 IN CATALYTICALLY-PRODUCTIVE JRNL TITL 2 TWIST-BOAT AND CHAIR CONFORMATIONS AND ASSOCIATES IN A JRNL TITL 3 LIGAND-DEPENDENT MANNER. JRNL REF INT.J.BIOL.MACROMOL. 52715 2026 JRNL REFN ISSN 0141-8130 JRNL PMID 42202926 JRNL DOI 10.1016/J.IJBIOMAC.2026.152715 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 86.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 31464 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.786 REMARK 3 FREE R VALUE TEST SET COUNT : 1506 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1886 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.3760 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.4240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1196 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 212 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06100 REMARK 3 B22 (A**2) : -0.06100 REMARK 3 B33 (A**2) : 0.19900 REMARK 3 B12 (A**2) : -0.03100 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.063 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.064 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.059 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.819 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1328 ; 0.011 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1202 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1815 ; 1.963 ; 1.867 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2782 ; 0.716 ; 1.791 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 159 ; 6.741 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 12 ; 8.385 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 233 ;13.793 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 191 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1562 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 304 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 247 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 30 ; 0.175 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 612 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 188 ; 0.202 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.039 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 621 ; 2.657 ; 2.409 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 621 ; 2.657 ; 2.409 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 785 ; 3.901 ; 4.317 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 786 ; 3.899 ; 4.316 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 707 ; 4.628 ; 3.015 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 668 ; 4.237 ; 2.909 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1030 ; 7.114 ; 5.324 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 988 ; 6.645 ; 5.113 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9T4D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1292151745. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97926 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 3.9.0 REMARK 200 DATA SCALING SOFTWARE : XIA2 3.9.0 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31754 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 86.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 16.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 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) : NULL REMARK 200 FOR SHELL : 0.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.9.02 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 20MG/ML PRECIPITANT REMARK 280 CONDITION: 29% PEG 6K, 0.1M NAOAC PH 5, 0.2M LICL, 10MM MGCL2, REMARK 280 20MM NAF RATIO: 1:1, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 11.48967 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 22.97933 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.23450 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.72417 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 5.74483 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 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 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 357 O HOH A 471 2.02 REMARK 500 OG SER A 148 O HOH A 301 2.16 REMARK 500 O HOH A 359 O HOH A 476 2.16 REMARK 500 O22 I7P A 201 O HOH A 302 2.18 REMARK 500 O32 I7P A 201 O HOH A 303 2.19 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 115 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 117 NE - CZ - NH2 ANGL. DEV. = -3.0 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 SER A 6 151.23 -48.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 115 0.09 SIDE CHAIN 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 A 509 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 510 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A 511 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A 512 DISTANCE = 6.82 ANGSTROMS 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 205 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 20 NH1 REMARK 620 2 VAL A 48 O 135.1 REMARK 620 3 HOH A 331 O 92.7 111.1 REMARK 620 4 HOH A 404 O 86.3 126.2 95.6 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 GLY A 50 O REMARK 620 2 GLU A 70 OE1 83.3 REMARK 620 3 I7P A 201 O34 166.6 88.8 REMARK 620 4 I7P A 201 O35 92.4 167.7 97.4 REMARK 620 5 I7P A 201 O65 101.8 79.0 87.2 90.6 REMARK 620 6 HOH A 331 O 82.9 90.3 86.3 100.6 167.6 REMARK 620 N 1 2 3 4 5 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 GLU A 66 OE1 REMARK 620 2 I7P A 201 O55 97.9 REMARK 620 3 HOH A 330 O 82.8 91.6 REMARK 620 4 HOH A 388 O 87.7 171.2 95.9 REMARK 620 5 HOH A 430 O 168.7 89.3 88.4 86.3 REMARK 620 N 1 2 3 4 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 OE2 REMARK 620 2 GLU A 70 OE1 90.9 REMARK 620 3 I7P A 201 O65 93.3 80.5 REMARK 620 4 HOH A 372 O 90.3 105.9 172.6 REMARK 620 5 HOH A 410 O 176.8 85.9 85.6 91.1 REMARK 620 N 1 2 3 4 DBREF 9T4D A 1 148 UNP O95989 NUDT3_HUMAN 1 148 SEQADV 9T4D ALA A 41 UNP O95989 ARG 41 ENGINEERED MUTATION 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 ALA 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 MG A 205 1 HET PO4 A 206 5 HET PO4 A 207 5 HET PO4 A 208 5 HET CL A 209 1 HET F A 210 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 PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION HETNAM F FLUORIDE 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 4(MG 2+) FORMUL 7 PO4 3(O4 P 3-) FORMUL 10 CL CL 1- FORMUL 11 F F 1- FORMUL 12 HOH *212(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 VAL A 100 N PHE A 26 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 NH1 ARG A 20 MG MG A 205 1555 1555 2.86 LINK O VAL A 48 MG MG A 205 1555 1555 2.73 LINK O GLY A 50 MG MG A 204 1555 1555 2.10 LINK OE1 GLU A 66 MG MG A 202 1555 1555 2.05 LINK OE2 GLU A 66 MG MG A 203 1555 1555 2.07 LINK OE1 GLU A 70 MG MG A 203 1555 1555 2.13 LINK OE1 GLU A 70 MG MG A 204 1555 1555 2.17 LINK O55 I7P A 201 MG MG A 202 1555 1555 2.01 LINK O65 I7P A 201 MG MG A 203 1555 1555 2.07 LINK O34 I7P A 201 MG MG A 204 1555 1555 2.07 LINK O35 I7P A 201 MG MG A 204 1555 1555 2.05 LINK O65 I7P A 201 MG MG A 204 1555 1555 2.09 LINK MG MG A 202 O HOH A 330 1555 1555 2.13 LINK MG MG A 202 O HOH A 388 1555 1555 2.17 LINK MG MG A 202 O HOH A 430 1555 1555 2.14 LINK MG MG A 203 O HOH A 372 1555 1555 1.95 LINK MG MG A 203 O HOH A 410 1555 1555 2.16 LINK MG MG A 204 O HOH A 331 1555 1555 2.12 LINK MG MG A 205 O HOH A 331 1555 1555 2.84 LINK MG MG A 205 O HOH A 404 1555 1555 2.77 CRYST1 99.950 99.950 34.469 90.00 90.00 120.00 P 61 6 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 0.010005 0.005776 0.000000 0.00000 SCALE2 0.000000 0.011553 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029012 0.00000 CONECT 177 1291 CONECT 393 1291 CONECT 407 1290 CONECT 529 1288 CONECT 530 1289 CONECT 560 1289 1290 CONECT 1248 1249 1253 1254 CONECT 1249 1248 1250 1255 CONECT 1250 1249 1251 1256 CONECT 1251 1250 1252 1257 CONECT 1252 1251 1253 1258 CONECT 1253 1248 1252 1259 CONECT 1254 1248 1281 CONECT 1255 1249 1282 CONECT 1256 1250 1283 CONECT 1257 1251 1284 CONECT 1258 1252 1285 CONECT 1259 1253 1286 CONECT 1260 1281 CONECT 1261 1282 CONECT 1262 1283 CONECT 1263 1284 CONECT 1264 1285 CONECT 1265 1286 CONECT 1266 1281 CONECT 1267 1282 CONECT 1268 1283 CONECT 1269 1284 1290 CONECT 1270 1285 1290 CONECT 1271 1286 CONECT 1272 1281 CONECT 1273 1282 CONECT 1274 1283 CONECT 1275 1284 CONECT 1276 1285 1287 CONECT 1277 1286 CONECT 1278 1287 1288 CONECT 1279 1287 1289 1290 CONECT 1280 1287 CONECT 1281 1254 1260 1266 1272 CONECT 1282 1255 1261 1267 1273 CONECT 1283 1256 1262 1268 1274 CONECT 1284 1257 1263 1269 1275 CONECT 1285 1258 1264 1270 1276 CONECT 1286 1259 1265 1271 1277 CONECT 1287 1276 1278 1279 1280 CONECT 1288 529 1278 1338 1396 CONECT 1288 1438 CONECT 1289 530 560 1279 1380 CONECT 1289 1418 CONECT 1290 407 560 1269 1270 CONECT 1290 1279 1339 CONECT 1291 177 393 1339 1412 CONECT 1292 1293 1294 1295 1296 CONECT 1293 1292 CONECT 1294 1292 CONECT 1295 1292 CONECT 1296 1292 CONECT 1297 1298 1299 1300 1301 CONECT 1298 1297 CONECT 1299 1297 CONECT 1300 1297 CONECT 1301 1297 CONECT 1302 1303 1304 1305 1306 CONECT 1303 1302 CONECT 1304 1302 CONECT 1305 1302 CONECT 1306 1302 CONECT 1338 1288 CONECT 1339 1290 1291 CONECT 1380 1289 CONECT 1396 1288 CONECT 1412 1291 CONECT 1418 1289 CONECT 1438 1288 MASTER 372 0 10 4 7 0 0 6 1469 1 75 12 END