HEADER TRANSFERASE 01-JUL-04 1W2D TITLE HUMAN INOSITOL (1,4,5)-TRISPHOSPHATE 3-KINASE COMPLEXED WITH TITLE 2 MN2+/ADP/INS(1,3,4,5)P4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INOSITOL-TRISPHOSPHATE 3-KINASE A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 197-461; COMPND 5 SYNONYM: INOSITOL 1,4,5-TRISPHOSPHATE 3-KINASE, IP3-3K; COMPND 6 EC: 2.1.7.127; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: POPTG KEYWDS INOSITOL PHOSPHATE KINASE, ADP, IP4, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.GONZALEZ,M.J.SCHELL,R.F.IRVINE,R.L.WILLIAMS REVDAT 4 08-MAY-24 1W2D 1 LINK REVDAT 3 24-JAN-18 1W2D 1 SOURCE REVDAT 2 24-FEB-09 1W2D 1 VERSN REVDAT 1 09-SEP-04 1W2D 0 JRNL AUTH B.GONZALEZ,M.J.SCHELL,A.J.LETCHER,D.B.VEPRINTSEV,R.F.IRVINE, JRNL AUTH 2 R.L.WILLIAMS JRNL TITL STRUCTURE OF A HUMAN INOSITOL 1,4,5-TRISPHOSPHATE 3-KINASE; JRNL TITL 2 SUBSTRATE BINDING REVEALS WHY IT IS NOT A PHOSPHOINOSITIDE JRNL TITL 3 3-KINASE JRNL REF MOL.CELL V. 15 689 2004 JRNL REFN ISSN 1097-2765 JRNL PMID 15350214 JRNL DOI 10.1016/J.MOLCEL.2004.08.004 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 46068 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2453 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) : 1.94 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3383 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2840 REMARK 3 BIN FREE R VALUE SET COUNT : 179 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4138 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 127 REMARK 3 SOLVENT ATOMS : 259 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.05000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : -0.96000 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): 0.181 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.167 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.125 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.260 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4339 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3919 ; 0.015 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5865 ; 1.751 ; 2.002 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9090 ; 0.981 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 511 ; 6.946 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 630 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4698 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 919 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 958 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4599 ; 0.261 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2444 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 262 ; 0.176 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 9 ; 0.195 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 58 ; 0.307 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.187 ; 0.200 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): 2547 ; 1.088 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4083 ; 1.866 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1792 ; 2.645 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1782 ; 3.999 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1W2D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1290015212. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48642 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 49.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 6.830 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5537 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.32 REMARK 200 R MERGE FOR SHELL (I) : 0.21000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.82 M NA CITRATE, 0.1 M NACL, 0.1 M REMARK 280 TRIS PH 8., PH 8.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 95.42200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 95.42200 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 36.02700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.70550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.02700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.70550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 95.42200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.02700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.70550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 95.42200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.02700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.70550 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PQS 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 B2059 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 ARG B 279 REMARK 465 GLU B 280 REMARK 465 ARG B 281 REMARK 465 PRO B 282 REMARK 465 GLU B 298 REMARK 465 ALA B 299 REMARK 465 PRO B 300 REMARK 465 THR B 301 REMARK 465 GLU B 302 REMARK 465 GLU B 303 REMARK 465 GLU B 304 REMARK 465 HIS B 305 REMARK 465 ALA B 306 REMARK 465 GLN B 307 REMARK 465 ARG B 308 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 VAL B 363 CB VAL B 363 CG1 -0.141 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 ASP A 253 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 268 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 287 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP B 287 CB - CG - OD2 ANGL. DEV. = 5.6 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 ARG A 240 -88.64 -128.43 REMARK 500 ARG A 281 74.82 -163.51 REMARK 500 ASP A 339 2.55 -66.20 REMARK 500 ARG A 350 -45.78 -134.02 REMARK 500 ASP A 416 83.27 69.30 REMARK 500 PRO A 424 150.23 -49.44 REMARK 500 ASP A 425 117.96 -30.84 REMARK 500 THR B 276 -47.59 -27.62 REMARK 500 ARG B 350 -47.35 -133.72 REMARK 500 ASP B 416 88.23 71.44 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 MN A1464 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 416 OD2 REMARK 620 2 4IP A1463 O5P 95.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B1464 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 416 OD2 REMARK 620 2 ADP B1462 O2A 82.7 REMARK 620 3 HOH B2129 O 81.1 100.0 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1464 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1465 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1466 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B1464 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1465 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A1462 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 4IP A1463 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B1462 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 4IP B1463 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1W2C RELATED DB: PDB REMARK 900 HUMAN INOSITOL (1,4,5) TRISPHOSPHATE 3- KINASE COMPLEXED WITH MN2+/ REMARK 900 AMPPNP/INS(1,4,5)P3 REMARK 900 RELATED ID: 1W2F RELATED DB: PDB REMARK 900 HUMAN INOSITOL (1,4,5)-TRISPHOSPHATE 3- KINASE SUBSTITUTED WITH REMARK 900 SELENOMETHIONINE DBREF 1W2D A 197 461 UNP P23677 IP3K_HUMAN 197 461 DBREF 1W2D B 197 461 UNP P23677 IP3K_HUMAN 197 461 SEQRES 1 A 265 SER PHE LYS ALA ALA GLY THR SER GLY LEU ILE LEU LYS SEQRES 2 A 265 ARG CYS SER GLU PRO GLU ARG TYR CYS LEU ALA ARG LEU SEQRES 3 A 265 MET ALA ASP ALA LEU ARG GLY CYS VAL PRO ALA PHE HIS SEQRES 4 A 265 GLY VAL VAL GLU ARG ASP GLY GLU SER TYR LEU GLN LEU SEQRES 5 A 265 GLN ASP LEU LEU ASP GLY PHE ASP GLY PRO CYS VAL LEU SEQRES 6 A 265 ASP CYS LYS MET GLY VAL ARG THR TYR LEU GLU GLU GLU SEQRES 7 A 265 LEU THR LYS ALA ARG GLU ARG PRO LYS LEU ARG LYS ASP SEQRES 8 A 265 MET TYR LYS LYS MET LEU ALA VAL ASP PRO GLU ALA PRO SEQRES 9 A 265 THR GLU GLU GLU HIS ALA GLN ARG ALA VAL THR LYS PRO SEQRES 10 A 265 ARG TYR MET GLN TRP ARG GLU GLY ILE SER SER SER THR SEQRES 11 A 265 THR LEU GLY PHE ARG ILE GLU GLY ILE LYS LYS ALA ASP SEQRES 12 A 265 GLY SER CYS SER THR ASP PHE LYS THR THR ARG SER ARG SEQRES 13 A 265 GLU GLN VAL LEU ARG VAL PHE GLU GLU PHE VAL GLN GLY SEQRES 14 A 265 ASP GLU GLU VAL LEU ARG ARG TYR LEU ASN ARG LEU GLN SEQRES 15 A 265 GLN ILE ARG ASP THR LEU GLU VAL SER GLU PHE PHE ARG SEQRES 16 A 265 ARG HIS GLU VAL ILE GLY SER SER LEU LEU PHE VAL HIS SEQRES 17 A 265 ASP HIS CYS HIS ARG ALA GLY VAL TRP LEU ILE ASP PHE SEQRES 18 A 265 GLY LYS THR THR PRO LEU PRO ASP GLY GLN ILE LEU ASP SEQRES 19 A 265 HIS ARG ARG PRO TRP GLU GLU GLY ASN ARG GLU ASP GLY SEQRES 20 A 265 TYR LEU LEU GLY LEU ASP ASN LEU ILE GLY ILE LEU ALA SEQRES 21 A 265 SER LEU ALA GLU ARG SEQRES 1 B 265 SER PHE LYS ALA ALA GLY THR SER GLY LEU ILE LEU LYS SEQRES 2 B 265 ARG CYS SER GLU PRO GLU ARG TYR CYS LEU ALA ARG LEU SEQRES 3 B 265 MET ALA ASP ALA LEU ARG GLY CYS VAL PRO ALA PHE HIS SEQRES 4 B 265 GLY VAL VAL GLU ARG ASP GLY GLU SER TYR LEU GLN LEU SEQRES 5 B 265 GLN ASP LEU LEU ASP GLY PHE ASP GLY PRO CYS VAL LEU SEQRES 6 B 265 ASP CYS LYS MET GLY VAL ARG THR TYR LEU GLU GLU GLU SEQRES 7 B 265 LEU THR LYS ALA ARG GLU ARG PRO LYS LEU ARG LYS ASP SEQRES 8 B 265 MET TYR LYS LYS MET LEU ALA VAL ASP PRO GLU ALA PRO SEQRES 9 B 265 THR GLU GLU GLU HIS ALA GLN ARG ALA VAL THR LYS PRO SEQRES 10 B 265 ARG TYR MET GLN TRP ARG GLU GLY ILE SER SER SER THR SEQRES 11 B 265 THR LEU GLY PHE ARG ILE GLU GLY ILE LYS LYS ALA ASP SEQRES 12 B 265 GLY SER CYS SER THR ASP PHE LYS THR THR ARG SER ARG SEQRES 13 B 265 GLU GLN VAL LEU ARG VAL PHE GLU GLU PHE VAL GLN GLY SEQRES 14 B 265 ASP GLU GLU VAL LEU ARG ARG TYR LEU ASN ARG LEU GLN SEQRES 15 B 265 GLN ILE ARG ASP THR LEU GLU VAL SER GLU PHE PHE ARG SEQRES 16 B 265 ARG HIS GLU VAL ILE GLY SER SER LEU LEU PHE VAL HIS SEQRES 17 B 265 ASP HIS CYS HIS ARG ALA GLY VAL TRP LEU ILE ASP PHE SEQRES 18 B 265 GLY LYS THR THR PRO LEU PRO ASP GLY GLN ILE LEU ASP SEQRES 19 B 265 HIS ARG ARG PRO TRP GLU GLU GLY ASN ARG GLU ASP GLY SEQRES 20 B 265 TYR LEU LEU GLY LEU ASP ASN LEU ILE GLY ILE LEU ALA SEQRES 21 B 265 SER LEU ALA GLU ARG HET ADP A1462 27 HET 4IP A1463 28 HET MN A1464 1 HET SO4 A1465 5 HET SO4 A1466 5 HET ADP B1462 27 HET 4IP B1463 28 HET MN B1464 1 HET SO4 B1465 5 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM SO4 SULFATE ION FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 4 4IP 2(C6 H16 O18 P4) FORMUL 5 MN 2(MN 2+) FORMUL 6 SO4 3(O4 S 2-) FORMUL 12 HOH *259(H2 O) HELIX 1 1 SER A 212 MET A 223 1 12 HELIX 2 2 ALA A 224 VAL A 231 5 8 HELIX 3 3 GLU A 272 ARG A 281 1 10 HELIX 4 4 ARG A 285 ASP A 296 1 12 HELIX 5 5 THR A 301 ARG A 308 1 8 HELIX 6 6 THR A 311 SER A 323 1 13 HELIX 7 7 SER A 324 GLY A 329 1 6 HELIX 8 8 SER A 351 GLN A 364 1 14 HELIX 9 9 ASP A 366 SER A 387 1 22 HELIX 10 10 SER A 387 ARG A 392 1 6 HELIX 11 11 GLY A 443 GLU A 460 1 18 HELIX 12 12 SER B 212 ALA B 224 1 13 HELIX 13 13 ASP B 225 VAL B 231 5 7 HELIX 14 14 GLU B 272 LYS B 277 1 6 HELIX 15 15 LYS B 286 ASP B 296 1 11 HELIX 16 16 THR B 311 SER B 323 1 13 HELIX 17 17 SER B 324 GLY B 329 1 6 HELIX 18 18 SER B 351 GLN B 364 1 14 HELIX 19 19 ASP B 366 SER B 387 1 22 HELIX 20 20 SER B 387 ARG B 392 1 6 HELIX 21 21 GLY B 443 GLU B 460 1 18 SHEET 1 AA 4 PHE A 198 ALA A 200 0 SHEET 2 AA 4 LEU A 206 ARG A 210 -1 O LEU A 208 N LYS A 199 SHEET 3 AA 4 SER A 244 GLN A 249 -1 O LEU A 246 N LYS A 209 SHEET 4 AA 4 PHE A 234 GLU A 239 -1 N HIS A 235 O GLN A 247 SHEET 1 AB 5 CYS A 342 SER A 343 0 SHEET 2 AB 5 PHE A 330 LYS A 336 -1 O ILE A 335 N SER A 343 SHEET 3 AB 5 CYS A 259 MET A 265 -1 O VAL A 260 N LYS A 336 SHEET 4 AB 5 SER A 399 HIS A 404 -1 O LEU A 400 N CYS A 263 SHEET 5 AB 5 ALA A 410 ILE A 415 -1 O GLY A 411 N VAL A 403 SHEET 1 AC 2 HIS A 393 ILE A 396 0 SHEET 2 AC 2 LYS A 419 PRO A 422 -1 O LYS A 419 N ILE A 396 SHEET 1 BA 4 PHE B 198 ALA B 200 0 SHEET 2 BA 4 LEU B 206 ARG B 210 -1 O LEU B 208 N LYS B 199 SHEET 3 BA 4 GLU B 243 GLN B 249 -1 O LEU B 246 N LYS B 209 SHEET 4 BA 4 PHE B 234 ARG B 240 -1 N HIS B 235 O GLN B 247 SHEET 1 BB 5 CYS B 342 SER B 343 0 SHEET 2 BB 5 PHE B 330 LYS B 336 -1 O ILE B 335 N SER B 343 SHEET 3 BB 5 CYS B 259 MET B 265 -1 O VAL B 260 N LYS B 336 SHEET 4 BB 5 SER B 399 HIS B 404 -1 O LEU B 400 N CYS B 263 SHEET 5 BB 5 ALA B 410 ILE B 415 -1 O GLY B 411 N VAL B 403 SHEET 1 BC 2 HIS B 393 VAL B 395 0 SHEET 2 BC 2 THR B 420 PRO B 422 -1 O THR B 421 N GLU B 394 LINK OD2 ASP A 416 MN MN A1464 1555 1555 2.77 LINK O5P 4IP A1463 MN MN A1464 1555 1555 2.43 LINK OD2 ASP B 416 MN MN B1464 1555 1555 2.29 LINK O2A ADP B1462 MN MN B1464 1555 1555 2.19 LINK MN MN B1464 O HOH B2129 1555 1555 2.39 SITE 1 AC1 4 ASP A 416 ADP A1462 4IP A1463 HOH A2105 SITE 1 AC2 4 ARG A 352 SER A 457 ARG A 461 HOH A2122 SITE 1 AC3 3 GLN A 354 ARG A 357 HOH A2129 SITE 1 AC4 4 ASP B 416 ADP B1462 4IP B1463 HOH B2129 SITE 1 AC5 3 GLN B 354 ARG B 357 HOH B2130 SITE 1 AC6 13 SER A 197 PHE A 198 LYS A 209 PRO A 232 SITE 2 AC6 13 GLN A 249 ASP A 250 LEU A 251 ASP A 262 SITE 3 AC6 13 LYS A 336 ASP A 416 MN A1464 HOH A2125 SITE 4 AC6 13 HOH A2126 SITE 1 AC7 12 LYS A 264 ARG A 285 MET A 288 LYS A 312 SITE 2 AC7 12 TYR A 315 MET A 316 ARG A 319 LYS A 419 SITE 3 AC7 12 MN A1464 HOH A2059 HOH A2127 HOH A2128 SITE 1 AC8 14 SER B 197 PHE B 198 LYS B 209 GLN B 249 SITE 2 AC8 14 ASP B 250 LEU B 251 ASP B 262 LYS B 336 SITE 3 AC8 14 LEU B 401 ASP B 416 MN B1464 HOH B2125 SITE 4 AC8 14 HOH B2126 HOH B2127 SITE 1 AC9 12 LYS B 264 ARG B 285 MET B 288 LYS B 291 SITE 2 AC9 12 LYS B 312 TYR B 315 MET B 316 ARG B 319 SITE 3 AC9 12 GLU B 333 LYS B 419 MN B1464 HOH B2128 CRYST1 72.054 97.411 190.844 90.00 90.00 90.00 C 2 2 21 16 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 0.013878 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010266 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005240 0.00000 MTRIX1 1 -0.210430 0.597060 0.774110 -61.59400 1 MTRIX2 1 0.585570 -0.557090 0.588860 8.62670 1 MTRIX3 1 0.782830 0.577210 -0.232390 56.44300 1