HEADER TRANSFERASE 07-JUL-23 8PPG TITLE HUMAN INOSITOL 1,4,5-TRISPHOSPHATE 3-KINASE A (IP3K) CATALYTIC DOMAIN TITLE 2 IN COMPLEX WITH BETA-D-GLUCOPYRANOSYL 1,3,4,6- TITLE 3 TETRAKISPHOSPHATE/ADP/MN AFTER REACTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: INOSITOL-TRISPHOSPHATE 3-KINASE A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: INOSITOL 1,4,5-TRISPHOSPHATE 3-KINASE A,IP3 3-KINASE A,IP3K COMPND 5 A,INSP 3-KINASE A; COMPND 6 EC: 2.7.1.127; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: CATALYTIC DOMAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ITPKA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: POPTG KEYWDS INOSITOL POLYPHOSPHATE, INSP, INOSITOL KINASE, IP3K, CALCIUM, INSP3, KEYWDS 2 IP3, IPK, IP3 3-K, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.A.MARQUEZ-MONINO,B.GONZALEZ REVDAT 2 27-MAR-24 8PPG 1 JRNL REVDAT 1 28-FEB-24 8PPG 0 JRNL AUTH M.A.MARQUEZ-MONINO,R.ORTEGA-GARCIA,H.WHITFIELD,A.M.RILEY, JRNL AUTH 2 L.INFANTES,S.W.GARRETT,M.L.SHIPTON,C.A.BREARLEY, JRNL AUTH 3 B.V.L.POTTER,B.GONZALEZ JRNL TITL SUBSTRATE PROMISCUITY OF INOSITOL 1,4,5-TRISPHOSPHATE KINASE JRNL TITL 2 DRIVEN BY STRUCTURALLY-MODIFIED LIGANDS AND ACTIVE SITE JRNL TITL 3 PLASTICITY. JRNL REF NAT COMMUN V. 15 1502 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38374076 JRNL DOI 10.1038/S41467-024-45917-5 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 95.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 63607 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3386 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4653 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.3510 REMARK 3 BIN FREE R VALUE SET COUNT : 257 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4144 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 158 REMARK 3 SOLVENT ATOMS : 339 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.12000 REMARK 3 B22 (A**2) : -0.99000 REMARK 3 B33 (A**2) : -2.13000 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): 0.119 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.118 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.665 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4432 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4015 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6005 ; 1.442 ; 1.653 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9284 ; 1.346 ; 1.589 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 522 ; 6.287 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 271 ;23.936 ;20.148 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 768 ;16.913 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 52 ;16.792 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 542 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4903 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1015 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): 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): 2088 ; 3.497 ; 4.449 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2087 ; 3.493 ; 4.447 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2610 ; 4.720 ; 6.651 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2611 ; 4.722 ; 6.652 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2344 ; 4.072 ; 4.958 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2325 ; 3.992 ; 4.927 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3369 ; 5.869 ; 7.249 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5136 ; 7.896 ;52.493 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5077 ; 7.816 ;52.256 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : NULL REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 0 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 2101 ; 0.54 ; 0.50 REMARK 3 TIGHT THERMAL 1 A (A**2): 1270 ; 3.97 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 2101 ; 4.50 ; 2.00 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 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 THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8PPG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292129661. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 0.8856 REMARK 200 MONOCHROMATOR : CHANNEL-CUT SI(111) REMARK 200 OPTICS : TOROIDAL MIRROR, ELLIPTICAL BEAM REMARK 200 SHAPE REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X CDTE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67053 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 190.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: CUBE / TRAPEZOIDAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.81 M SODIUM CITRATE, 0.1M TRIS PH REMARK 280 8.5 AND 0.1 M NACL. PROTEIN:PRECIPITANT RATIO 1:1. PROTEIN REMARK 280 CONCENTRATION: 17 MG/ML. PROTEIN BUFFER: 20 MM TRIS PH 7.5, 50 REMARK 280 MM AMMONIUM SULFATE AND 2 MM DTT. SOAKING OVERNIGHT WITH 1.5 M REMARK 280 LITHIUM SULFATE, 0.1 M TRIS PH 8.5, 7 MM BETA-D-GLUCOPYRANOSYL 1, REMARK 280 3,4-TRISPHOSPHATE (SUBSTRATE), 10 MM ATP AND 10 MM MNCL2., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 95.37750 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 95.37750 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 35.64150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.55100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.64150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.55100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 95.37750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.64150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.55100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 95.37750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.64150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.55100 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 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 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 S SO4 B 702 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 949 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 LEU A 191 REMARK 465 ALA A 192 REMARK 465 GLY A 193 REMARK 465 HIS A 194 REMARK 465 THR A 195 REMARK 465 GLY B 193 REMARK 465 HIS B 194 REMARK 465 LYS B 277 REMARK 465 ALA B 278 REMARK 465 ARG B 279 REMARK 465 GLU B 280 REMARK 465 ARG B 281 REMARK 465 PRO B 282 REMARK 465 LYS B 283 REMARK 465 LEU B 284 REMARK 465 ARG B 285 REMARK 465 LYS B 286 REMARK 465 ASP B 287 REMARK 465 MET B 288 REMARK 465 TYR B 289 REMARK 465 LYS B 290 REMARK 465 LYS B 291 REMARK 465 MET B 292 REMARK 465 LEU B 293 REMARK 465 ALA B 294 REMARK 465 VAL B 295 REMARK 465 ASP B 296 REMARK 465 PRO B 297 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 465 ALA B 309 REMARK 465 VAL B 310 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 184 136.69 -174.08 REMARK 500 ARG A 281 71.19 -172.38 REMARK 500 LYS A 283 79.55 -104.28 REMARK 500 ARG A 350 -45.72 -135.39 REMARK 500 ASP A 416 84.28 76.20 REMARK 500 ASP A 425 -126.31 43.44 REMARK 500 ARG B 350 -46.67 -134.04 REMARK 500 ASP B 416 85.88 79.68 REMARK 500 ASP B 425 133.00 -39.15 REMARK 500 GLU B 437 121.78 -38.75 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 A 706 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 416 OD2 REMARK 620 2 ADP A 704 O1B 87.8 REMARK 620 3 ADP A 704 O1A 94.1 75.6 REMARK 620 4 46I A 705 O16 98.5 86.3 157.5 REMARK 620 5 HOH A 861 O 87.7 175.1 106.6 92.6 REMARK 620 6 HOH A 897 O 169.5 102.7 87.7 83.3 81.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 707 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 416 OD1 REMARK 620 2 ASP A 416 OD2 52.4 REMARK 620 3 ADP A 704 O2B 83.2 77.1 REMARK 620 4 HOH A 816 O 75.6 84.5 157.7 REMARK 620 5 HOH A 882 O 143.5 91.5 95.0 97.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 705 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 416 OD2 REMARK 620 2 ADP B 703 O1B 91.9 REMARK 620 3 ADP B 703 O1A 101.8 84.5 REMARK 620 4 HOH B 802 O 80.5 81.5 165.9 REMARK 620 5 HOH B 831 O 91.5 174.5 99.1 94.7 REMARK 620 6 HOH B 902 O 171.2 90.0 86.9 91.3 86.0 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8PP8 RELATED DB: PDB REMARK 900 SAME PROTEIN, DIFFERENT LIGAND. REMARK 900 RELATED ID: 8PP9 RELATED DB: PDB REMARK 900 SAME PROTEIN, DIFFERENT LIGAND. REMARK 900 RELATED ID: 8PPA RELATED DB: PDB REMARK 900 SAME PROTEIN, DIFFERENT LIGAND. REMARK 900 RELATED ID: 8PPB RELATED DB: PDB REMARK 900 SAME PROTEIN, DIFFERENT LIGAND. REMARK 900 RELATED ID: 8PPC RELATED DB: PDB REMARK 900 SAME PROTEIN, DIFFERENT LIGAND. REMARK 900 RELATED ID: 8PPD RELATED DB: PDB REMARK 900 SAME PROTEIN, DIFFERENT LIGAND. REMARK 900 RELATED ID: 8PPE RELATED DB: PDB REMARK 900 SAME PROTEIN, DIFFERENT LIGAND. REMARK 900 RELATED ID: 8PPF RELATED DB: PDB REMARK 900 SAME PROTEIN, DIFFERENT LIGAND. DBREF 8PPG A 188 461 UNP P23677 IP3KA_HUMAN 188 461 DBREF 8PPG B 188 461 UNP P23677 IP3KA_HUMAN 188 461 SEQADV 8PPG GLY A 183 UNP P23677 EXPRESSION TAG SEQADV 8PPG SER A 184 UNP P23677 EXPRESSION TAG SEQADV 8PPG HIS A 185 UNP P23677 EXPRESSION TAG SEQADV 8PPG MET A 186 UNP P23677 EXPRESSION TAG SEQADV 8PPG SER A 187 UNP P23677 EXPRESSION TAG SEQADV 8PPG GLY B 183 UNP P23677 EXPRESSION TAG SEQADV 8PPG SER B 184 UNP P23677 EXPRESSION TAG SEQADV 8PPG HIS B 185 UNP P23677 EXPRESSION TAG SEQADV 8PPG MET B 186 UNP P23677 EXPRESSION TAG SEQADV 8PPG SER B 187 UNP P23677 EXPRESSION TAG SEQRES 1 A 279 GLY SER HIS MET SER TRP VAL GLN LEU ALA GLY HIS THR SEQRES 2 A 279 GLY SER PHE LYS ALA ALA GLY THR SER GLY LEU ILE LEU SEQRES 3 A 279 LYS ARG CYS SER GLU PRO GLU ARG TYR CYS LEU ALA ARG SEQRES 4 A 279 LEU MET ALA ASP ALA LEU ARG GLY CYS VAL PRO ALA PHE SEQRES 5 A 279 HIS GLY VAL VAL GLU ARG ASP GLY GLU SER TYR LEU GLN SEQRES 6 A 279 LEU GLN ASP LEU LEU ASP GLY PHE ASP GLY PRO CYS VAL SEQRES 7 A 279 LEU ASP CYS LYS MET GLY VAL ARG THR TYR LEU GLU GLU SEQRES 8 A 279 GLU LEU THR LYS ALA ARG GLU ARG PRO LYS LEU ARG LYS SEQRES 9 A 279 ASP MET TYR LYS LYS MET LEU ALA VAL ASP PRO GLU ALA SEQRES 10 A 279 PRO THR GLU GLU GLU HIS ALA GLN ARG ALA VAL THR LYS SEQRES 11 A 279 PRO ARG TYR MET GLN TRP ARG GLU GLY ILE SER SER SER SEQRES 12 A 279 THR THR LEU GLY PHE ARG ILE GLU GLY ILE LYS LYS ALA SEQRES 13 A 279 ASP GLY SER CYS SER THR ASP PHE LYS THR THR ARG SER SEQRES 14 A 279 ARG GLU GLN VAL LEU ARG VAL PHE GLU GLU PHE VAL GLN SEQRES 15 A 279 GLY ASP GLU GLU VAL LEU ARG ARG TYR LEU ASN ARG LEU SEQRES 16 A 279 GLN GLN ILE ARG ASP THR LEU GLU VAL SER GLU PHE PHE SEQRES 17 A 279 ARG ARG HIS GLU VAL ILE GLY SER SER LEU LEU PHE VAL SEQRES 18 A 279 HIS ASP HIS CYS HIS ARG ALA GLY VAL TRP LEU ILE ASP SEQRES 19 A 279 PHE GLY LYS THR THR PRO LEU PRO ASP GLY GLN ILE LEU SEQRES 20 A 279 ASP HIS ARG ARG PRO TRP GLU GLU GLY ASN ARG GLU ASP SEQRES 21 A 279 GLY TYR LEU LEU GLY LEU ASP ASN LEU ILE GLY ILE LEU SEQRES 22 A 279 ALA SER LEU ALA GLU ARG SEQRES 1 B 279 GLY SER HIS MET SER TRP VAL GLN LEU ALA GLY HIS THR SEQRES 2 B 279 GLY SER PHE LYS ALA ALA GLY THR SER GLY LEU ILE LEU SEQRES 3 B 279 LYS ARG CYS SER GLU PRO GLU ARG TYR CYS LEU ALA ARG SEQRES 4 B 279 LEU MET ALA ASP ALA LEU ARG GLY CYS VAL PRO ALA PHE SEQRES 5 B 279 HIS GLY VAL VAL GLU ARG ASP GLY GLU SER TYR LEU GLN SEQRES 6 B 279 LEU GLN ASP LEU LEU ASP GLY PHE ASP GLY PRO CYS VAL SEQRES 7 B 279 LEU ASP CYS LYS MET GLY VAL ARG THR TYR LEU GLU GLU SEQRES 8 B 279 GLU LEU THR LYS ALA ARG GLU ARG PRO LYS LEU ARG LYS SEQRES 9 B 279 ASP MET TYR LYS LYS MET LEU ALA VAL ASP PRO GLU ALA SEQRES 10 B 279 PRO THR GLU GLU GLU HIS ALA GLN ARG ALA VAL THR LYS SEQRES 11 B 279 PRO ARG TYR MET GLN TRP ARG GLU GLY ILE SER SER SER SEQRES 12 B 279 THR THR LEU GLY PHE ARG ILE GLU GLY ILE LYS LYS ALA SEQRES 13 B 279 ASP GLY SER CYS SER THR ASP PHE LYS THR THR ARG SER SEQRES 14 B 279 ARG GLU GLN VAL LEU ARG VAL PHE GLU GLU PHE VAL GLN SEQRES 15 B 279 GLY ASP GLU GLU VAL LEU ARG ARG TYR LEU ASN ARG LEU SEQRES 16 B 279 GLN GLN ILE ARG ASP THR LEU GLU VAL SER GLU PHE PHE SEQRES 17 B 279 ARG ARG HIS GLU VAL ILE GLY SER SER LEU LEU PHE VAL SEQRES 18 B 279 HIS ASP HIS CYS HIS ARG ALA GLY VAL TRP LEU ILE ASP SEQRES 19 B 279 PHE GLY LYS THR THR PRO LEU PRO ASP GLY GLN ILE LEU SEQRES 20 B 279 ASP HIS ARG ARG PRO TRP GLU GLU GLY ASN ARG GLU ASP SEQRES 21 B 279 GLY TYR LEU LEU GLY LEU ASP ASN LEU ILE GLY ILE LEU SEQRES 22 B 279 ALA SER LEU ALA GLU ARG HET SO4 A 701 5 HET SO4 A 702 5 HET SO4 A 703 5 HET ADP A 704 27 HET 46I A 705 28 HET MN A 706 1 HET MN A 707 1 HET SO4 A 708 5 HET SO4 B 701 5 HET SO4 B 702 5 HET ADP B 703 27 HET 46I B 704 28 HET MN B 705 1 HET SO4 B 706 5 HET SO4 B 707 5 HET SO4 B 708 5 HETNAM SO4 SULFATE ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM 46I BETA-D-GLUCOPYRANOSYL 1,3,4,6-TETRAKISPHOSPHATE HETNAM MN MANGANESE (II) ION HETSYN 46I [(2S,3R,4R,5R,6R)-3-OXIDANYL-2,5-DIPHOSPHONOOXY-6- HETSYN 2 46I (PHOSPHONOOXYMETHYL)OXAN-4-YL] DIHYDROGEN PHOSPHATE FORMUL 3 SO4 9(O4 S 2-) FORMUL 6 ADP 2(C10 H15 N5 O10 P2) FORMUL 7 46I 2(C6 H16 O18 P4) FORMUL 8 MN 3(MN 2+) FORMUL 19 HOH *339(H2 O) HELIX 1 AA1 SER A 184 GLN A 190 1 7 HELIX 2 AA2 SER A 212 MET A 223 1 12 HELIX 3 AA3 ALA A 224 VAL A 231 5 8 HELIX 4 AA4 GLU A 272 ARG A 281 1 10 HELIX 5 AA5 ARG A 285 ASP A 296 1 12 HELIX 6 AA6 THR A 301 ARG A 308 1 8 HELIX 7 AA7 THR A 311 SER A 323 1 13 HELIX 8 AA8 SER A 324 GLY A 329 1 6 HELIX 9 AA9 SER A 351 GLN A 364 1 14 HELIX 10 AB1 ASP A 366 SER A 387 1 22 HELIX 11 AB2 SER A 387 ARG A 392 1 6 HELIX 12 AB3 GLY A 443 GLU A 460 1 18 HELIX 13 AB4 SER B 184 ALA B 192 1 9 HELIX 14 AB5 SER B 212 ALA B 224 1 13 HELIX 15 AB6 ASP B 225 VAL B 231 5 7 HELIX 16 AB7 LEU B 271 LEU B 275 5 5 HELIX 17 AB8 LYS B 312 SER B 323 1 12 HELIX 18 AB9 SER B 324 GLY B 329 1 6 HELIX 19 AC1 SER B 351 GLN B 364 1 14 HELIX 20 AC2 ASP B 366 SER B 387 1 22 HELIX 21 AC3 SER B 387 ARG B 392 1 6 HELIX 22 AC4 GLY B 443 GLU B 460 1 18 SHEET 1 AA1 4 PHE A 198 ALA A 200 0 SHEET 2 AA1 4 LEU A 206 ARG A 210 -1 O LEU A 208 N LYS A 199 SHEET 3 AA1 4 SER A 244 GLN A 249 -1 O LEU A 246 N LYS A 209 SHEET 4 AA1 4 PHE A 234 GLU A 239 -1 N VAL A 238 O TYR A 245 SHEET 1 AA2 5 CYS A 342 SER A 343 0 SHEET 2 AA2 5 PHE A 330 LYS A 336 -1 N ILE A 335 O SER A 343 SHEET 3 AA2 5 CYS A 259 MET A 265 -1 N VAL A 260 O LYS A 336 SHEET 4 AA2 5 SER A 399 HIS A 404 -1 O HIS A 404 N CYS A 259 SHEET 5 AA2 5 ALA A 410 ILE A 415 -1 O TRP A 413 N LEU A 401 SHEET 1 AA3 2 HIS A 393 GLU A 394 0 SHEET 2 AA3 2 THR A 421 PRO A 422 -1 O THR A 421 N GLU A 394 SHEET 1 AA4 4 PHE B 198 ALA B 200 0 SHEET 2 AA4 4 LEU B 206 ARG B 210 -1 O LEU B 208 N LYS B 199 SHEET 3 AA4 4 GLU B 243 GLN B 249 -1 O LEU B 246 N LYS B 209 SHEET 4 AA4 4 PHE B 234 ARG B 240 -1 N VAL B 238 O TYR B 245 SHEET 1 AA5 5 CYS B 342 SER B 343 0 SHEET 2 AA5 5 PHE B 330 LYS B 336 -1 N ILE B 335 O SER B 343 SHEET 3 AA5 5 CYS B 259 MET B 265 -1 N VAL B 260 O LYS B 336 SHEET 4 AA5 5 SER B 399 HIS B 404 -1 O HIS B 404 N CYS B 259 SHEET 5 AA5 5 ALA B 410 ILE B 415 -1 O TRP B 413 N LEU B 401 SHEET 1 AA6 2 HIS B 393 ILE B 396 0 SHEET 2 AA6 2 LYS B 419 PRO B 422 -1 O THR B 421 N GLU B 394 LINK OD2 ASP A 416 MN MN A 706 1555 1555 2.19 LINK OD1 ASP A 416 MN MN A 707 1555 1555 2.56 LINK OD2 ASP A 416 MN MN A 707 1555 1555 2.49 LINK O1B ADP A 704 MN MN A 706 1555 1555 2.39 LINK O1A ADP A 704 MN MN A 706 1555 1555 2.16 LINK O2B ADP A 704 MN MN A 707 1555 1555 2.65 LINK O16 46I A 705 MN MN A 706 1555 1555 2.68 LINK MN MN A 706 O HOH A 861 1555 1555 2.28 LINK MN MN A 706 O HOH A 897 1555 1555 2.29 LINK MN MN A 707 O HOH A 816 1555 1555 2.69 LINK MN MN A 707 O HOH A 882 1555 1555 2.35 LINK OD2 ASP B 416 MN MN B 705 1555 1555 1.96 LINK O1B ADP B 703 MN MN B 705 1555 1555 2.28 LINK O1A ADP B 703 MN MN B 705 1555 1555 2.22 LINK MN MN B 705 O HOH B 802 1555 1555 2.40 LINK MN MN B 705 O HOH B 831 1555 1555 2.37 LINK MN MN B 705 O HOH B 902 1555 1555 1.85 CRYST1 71.283 97.102 190.755 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 0.014029 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010298 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005242 0.00000