HEADER HYDROLASE 30-OCT-25 9T4K TITLE HUMAN DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 1 (DIPP1) H91M TITLE 2 MUTANT IN COMPLEX WITH IP6 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 KEYWDS INOSITOL METABOLISM, PHOSPHATASE, NUDIX HYDROLASES, DIPP1, IP6, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.CASAS-FLOREZ,M.A.MARQUEZ-MONINO,B.GONZALEZ REVDAT 1 10-JUN-26 9T4K 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. 1.39 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) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 72.5 REMARK 3 NUMBER OF REFLECTIONS : 26071 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) : 0.187 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.921 REMARK 3 FREE R VALUE TEST SET COUNT : 1283 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.39 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.43 REMARK 3 REFLECTION IN BIN (WORKING SET) : 146 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 5.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.4450 REMARK 3 BIN FREE R VALUE SET COUNT : 5 REMARK 3 BIN FREE R VALUE : 0.5230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1200 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 187 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00500 REMARK 3 B22 (A**2) : 0.04400 REMARK 3 B33 (A**2) : -0.05000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.084 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.054 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.417 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1368 ; 0.011 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1255 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1869 ; 1.945 ; 1.874 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2912 ; 0.683 ; 1.784 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 167 ; 7.272 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 12 ;11.806 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 245 ;13.539 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 203 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1617 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 309 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 247 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 27 ; 0.164 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 610 ; 0.180 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 142 ; 0.226 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.168 ; 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): 644 ; 2.347 ; 1.699 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 644 ; 2.347 ; 1.699 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 819 ; 3.796 ; 3.037 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 820 ; 3.794 ; 3.037 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 724 ; 3.444 ; 2.302 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 721 ; 3.446 ; 2.287 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1050 ; 5.585 ; 4.033 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1045 ; 5.591 ; 4.002 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 9T4K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1292151738. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-23 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 : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.88560 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC 1.1.7 REMARK 200 DATA SCALING SOFTWARE : AUTOPROC 1.1.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26701 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 39.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 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 : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.8.0419 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 19.5MG/ML IP6: 10MM REMARK 280 PRECIPITANT CONDITION: 32% PEG 6K, 0.1M NAOAC PH 5, 0.2M LICL, REMARK 280 1MM MGCL2 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 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 17.20600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.32200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.43450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.32200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.20600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.43450 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 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 O26 IHP A 201 O HOH A 301 1.94 REMARK 500 O HOH A 398 O HOH A 434 2.07 REMARK 500 N MET A 1 O HOH A 302 2.09 REMARK 500 O HOH A 320 O HOH A 355 2.15 REMARK 500 O HOH A 365 O HOH A 456 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 CYS A 23 N - CA - CB ANGL. DEV. = 10.4 DEGREES REMARK 500 ARG A 27 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 115 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 115 NE - CZ - NH2 ANGL. DEV. = -4.9 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 LEU A 4 59.35 -108.49 REMARK 500 ARG A 41 -44.72 -131.43 REMARK 500 ARG A 41 -41.11 -131.43 REMARK 500 ASP A 44 -9.78 76.50 REMARK 500 LYS A 133 67.56 -155.45 REMARK 500 LEU A 143 -61.65 -106.31 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 27 0.14 SIDE CHAIN REMARK 500 ARG A 115 0.10 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 487 DISTANCE = 6.72 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 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 50 O REMARK 620 2 GLU A 70 OE1 78.4 REMARK 620 3 IHP A 201 O32 89.6 167.9 REMARK 620 4 IHP A 201 O23 163.9 94.9 97.0 REMARK 620 5 PO4 A 202 O2 98.3 77.3 103.6 94.4 REMARK 620 6 HOH A 338 O 79.2 83.3 95.6 85.5 160.6 REMARK 620 N 1 2 3 4 5 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 GLU A 66 OE2 REMARK 620 2 GLU A 70 OE1 85.2 REMARK 620 3 PO4 A 202 O2 89.1 89.0 REMARK 620 4 PO4 A 202 O3 75.1 142.5 59.6 REMARK 620 5 HOH A 317 O 81.5 116.3 151.9 92.3 REMARK 620 6 HOH A 439 O 153.4 94.3 117.5 117.4 74.9 REMARK 620 N 1 2 3 4 5 DBREF 9T4K A 1 148 UNP O95989 NUDT3_HUMAN 1 148 SEQADV 9T4K MET A 91 UNP O95989 HIS 91 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 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 MET 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 IHP A 201 36 HET PO4 A 202 5 HET EDO A 203 4 HET MG A 204 1 HET MG A 205 1 HET PO4 A 206 5 HET CL A 207 1 HETNAM IHP INOSITOL HEXAKISPHOSPHATE HETNAM PO4 PHOSPHATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETSYN IHP MYO-INOSITOL HEXAKISPHOSPHATE; INOSITOL 1,2,3,4,5,6- HETSYN 2 IHP HEXAKISPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 IHP C6 H18 O24 P6 FORMUL 3 PO4 2(O4 P 3-) FORMUL 4 EDO C2 H6 O2 FORMUL 5 MG 2(MG 2+) FORMUL 8 CL CL 1- FORMUL 9 HOH *187(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 LYS A 133 1 12 HELIX 4 AA4 LYS A 133 SER A 138 1 6 HELIX 5 AA5 TYR A 139 GLU A 141 5 3 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 MET A 91 VAL A 103 1 O TYR A 96 N LEU A 24 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 204 1555 1555 2.28 LINK OE2 GLU A 66 MG MG A 205 1555 1555 2.57 LINK OE1 GLU A 70 MG MG A 204 1555 1555 2.28 LINK OE1 GLU A 70 MG MG A 205 1555 1555 2.19 LINK O32 IHP A 201 MG MG A 204 1555 1555 2.20 LINK O23 IHP A 201 MG MG A 204 1555 1555 2.30 LINK O2 PO4 A 202 MG MG A 204 1555 1555 2.18 LINK O2 PO4 A 202 MG MG A 205 1555 1555 1.77 LINK O3 PO4 A 202 MG MG A 205 1555 1555 2.92 LINK MG MG A 204 O HOH A 338 1555 1555 2.23 LINK MG MG A 205 O HOH A 317 1555 1555 1.89 LINK MG MG A 205 O HOH A 439 1555 1555 2.41 CRYST1 34.412 64.869 78.644 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 0.029060 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015416 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012716 0.00000 CONECT 458 1334 CONECT 574 1335 CONECT 611 1334 1335 CONECT 1289 1290 1294 1295 CONECT 1290 1289 1291 1300 CONECT 1291 1290 1292 1305 CONECT 1292 1291 1293 1310 CONECT 1293 1292 1294 1315 CONECT 1294 1289 1293 1320 CONECT 1295 1289 1296 CONECT 1296 1295 1297 1298 1299 CONECT 1297 1296 CONECT 1298 1296 CONECT 1299 1296 CONECT 1300 1290 1301 CONECT 1301 1300 1302 1303 1304 CONECT 1302 1301 CONECT 1303 1301 1334 CONECT 1304 1301 CONECT 1305 1291 1306 CONECT 1306 1305 1307 1308 1309 CONECT 1307 1306 1334 CONECT 1308 1306 CONECT 1309 1306 CONECT 1310 1292 1311 CONECT 1311 1310 1312 1313 1314 CONECT 1312 1311 CONECT 1313 1311 CONECT 1314 1311 CONECT 1315 1293 1316 CONECT 1316 1315 1317 1318 1319 CONECT 1317 1316 CONECT 1318 1316 CONECT 1319 1316 CONECT 1320 1294 1321 CONECT 1321 1320 1322 1323 1324 CONECT 1322 1321 CONECT 1323 1321 CONECT 1324 1321 CONECT 1325 1326 1327 1328 1329 CONECT 1326 1325 CONECT 1327 1325 1334 1335 CONECT 1328 1325 1335 CONECT 1329 1325 CONECT 1330 1331 1332 CONECT 1331 1330 CONECT 1332 1330 1333 CONECT 1333 1332 CONECT 1334 458 611 1303 1307 CONECT 1334 1327 1379 CONECT 1335 574 611 1327 1328 CONECT 1335 1358 1481 CONECT 1336 1337 1338 1339 1340 CONECT 1337 1336 CONECT 1338 1336 CONECT 1339 1336 CONECT 1340 1336 CONECT 1358 1335 CONECT 1379 1334 CONECT 1481 1335 MASTER 351 0 7 5 7 0 0 6 1440 1 60 12 END