HEADER TRANSFERASE 02-AUG-11 3T9F TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN DIPHOSPHOINOSITOL TITLE 2 PENTAKISPHOSPHATE KINASE 2 (PPIP5K2) IN COMPLEX WITH ADP AND 1,5- TITLE 3 (PP)2-IP4 (1,5-IP8) COMPND MOL_ID: 1; COMPND 2 MOLECULE: INOSITOL PYROPHOSPHATE KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ATP-GRASP KINASE DOMAIN; COMPND 5 EC: 2.7.4.24; COMPND 6 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: PPIP5K2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ARCTIC EXPRESS (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST566 KEYWDS ATP-GRASP FOLD, INOSITOL PYROPHOSPHATE KINASE, PHOSPHORYL KEYWDS 2 TRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,J.FALCK,T.M.T.HALL,S.B.SHEARS REVDAT 4 28-FEB-24 3T9F 1 REMARK SEQADV LINK REVDAT 3 11-JAN-12 3T9F 1 JRNL REVDAT 2 14-DEC-11 3T9F 1 JRNL REVDAT 1 07-DEC-11 3T9F 0 JRNL AUTH H.WANG,J.R.FALCK,T.M.HALL,S.B.SHEARS JRNL TITL STRUCTURAL BASIS FOR AN INOSITOL PYROPHOSPHATE KINASE JRNL TITL 2 SURMOUNTING PHOSPHATE CROWDING. JRNL REF NAT.CHEM.BIOL. V. 8 111 2011 JRNL REFN ISSN 1552-4450 JRNL PMID 22119861 JRNL DOI 10.1038/NCHEMBIO.733 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 24344 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : EQUIVALENT AND EXPANDED REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1606 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1706 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.1890 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2547 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.44000 REMARK 3 B22 (A**2) : 0.11000 REMARK 3 B33 (A**2) : -0.55000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.160 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.092 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.265 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2735 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3732 ; 1.390 ; 2.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 331 ; 5.571 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;37.300 ;24.160 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 471 ;13.587 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;15.688 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 410 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2056 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1625 ; 0.700 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2650 ; 1.330 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1110 ; 2.036 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1080 ; 3.331 ; 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 : 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: NULL REMARK 4 REMARK 4 3T9F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067203. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26099 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12600 REMARK 200 FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 33.7000 REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% (W/V) PEG 3350, 20 MM MGCL2, 0.1 M REMARK 280 HEPES, PH 7.0, 1 MM ATP, 2 MM CDCL2, SOAKING WITH 5-IP7 UNDER PH REMARK 280 5.2 FOR 2 DAYS , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 44.51800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.74200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.00450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.74200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.51800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.00450 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 GLY A 37 REMARK 465 SER A 38 REMARK 465 PHE A 39 REMARK 465 THR A 40 REMARK 465 GLU A 41 REMARK 465 ARG A 42 REMARK 465 PRO A 361 REMARK 465 LEU A 362 REMARK 465 GLU A 363 REMARK 465 ALA A 364 REMARK 465 GLU A 365 REMARK 465 ASP A 366 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 OE1 GLU A 174 O HOH A 466 2.17 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 348 NE - CZ - NH1 ANGL. DEV. = 3.4 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 ASP A 268 -3.50 -147.18 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 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 22 O REMARK 620 2 ASP A 309 OD2 83.0 REMARK 620 3 ASP A 321 OD2 174.7 92.8 REMARK 620 4 ADP A 401 O3B 93.8 176.7 90.4 REMARK 620 5 ADP A 401 O2A 91.7 92.2 91.8 87.0 REMARK 620 6 I8P A 501 O61 92.0 96.8 85.1 84.2 170.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 68 O REMARK 620 2 PHE A 70 O 94.8 REMARK 620 3 ILE A 73 O 129.6 94.8 REMARK 620 4 HOH A 508 O 78.9 83.5 151.4 REMARK 620 5 HOH A 556 O 87.6 174.6 87.4 92.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 606 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 251 OG1 REMARK 620 2 GLN A 303 O 164.2 REMARK 620 3 THR A 304 O 89.0 85.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 601 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 321 OD2 REMARK 620 2 ASP A 321 OD1 51.6 REMARK 620 3 ASN A 323 OD1 90.9 83.3 REMARK 620 4 HOH A 399 O 155.6 104.1 83.8 REMARK 620 5 ADP A 401 O2B 87.8 90.8 173.3 94.6 REMARK 620 6 I8P A 501 O51 99.7 150.5 91.6 104.3 95.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 604 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 369 O REMARK 620 2 I8P A 501 O35 93.9 REMARK 620 3 I8P A 501 O44 93.1 98.0 REMARK 620 4 HOH A 534 O 170.8 91.7 93.4 REMARK 620 5 HOH A 549 O 91.4 171.5 88.2 82.2 REMARK 620 6 HOH A 610 O 86.9 83.4 178.5 86.5 90.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 605 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 480 O REMARK 620 2 HOH A 483 O 81.1 REMARK 620 3 HOH A 517 O 93.7 161.7 REMARK 620 4 HOH A 524 O 79.5 83.8 112.7 REMARK 620 5 HOH A 599 O 163.4 82.5 102.7 96.1 REMARK 620 6 HOH A 700 O 91.8 82.0 80.7 164.3 88.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE I8P A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 606 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3T54 RELATED DB: PDB REMARK 900 RELATED ID: 3T7A RELATED DB: PDB REMARK 900 RELATED ID: 3T99 RELATED DB: PDB REMARK 900 RELATED ID: 3T9A RELATED DB: PDB REMARK 900 RELATED ID: 3T9B RELATED DB: PDB REMARK 900 RELATED ID: 3T9C RELATED DB: PDB REMARK 900 RELATED ID: 3T9D RELATED DB: PDB REMARK 900 RELATED ID: 3T9E RELATED DB: PDB DBREF 3T9F A 41 366 UNP O43314 VIP2_HUMAN 41 366 SEQADV 3T9F GLY A 37 UNP O43314 EXPRESSION TAG SEQADV 3T9F SER A 38 UNP O43314 EXPRESSION TAG SEQADV 3T9F PHE A 39 UNP O43314 EXPRESSION TAG SEQADV 3T9F THR A 40 UNP O43314 EXPRESSION TAG SEQRES 1 A 330 GLY SER PHE THR GLU ARG GLN ILE VAL VAL GLY ILE CYS SEQRES 2 A 330 SER MET ALA LYS LYS SER LYS SER LYS PRO MET LYS GLU SEQRES 3 A 330 ILE LEU GLU ARG ILE SER LEU PHE LYS TYR ILE THR VAL SEQRES 4 A 330 VAL VAL PHE GLU GLU GLU VAL ILE LEU ASN GLU PRO VAL SEQRES 5 A 330 GLU ASN TRP PRO LEU CYS ASP CYS LEU ILE SER PHE HIS SEQRES 6 A 330 SER LYS GLY PHE PRO LEU ASP LYS ALA VAL ALA TYR ALA SEQRES 7 A 330 LYS LEU ARG ASN PRO PHE VAL ILE ASN ASP LEU ASN MET SEQRES 8 A 330 GLN TYR LEU ILE GLN ASP ARG ARG GLU VAL TYR SER ILE SEQRES 9 A 330 LEU GLN ALA GLU GLY ILE LEU LEU PRO ARG TYR ALA ILE SEQRES 10 A 330 LEU ASN ARG ASP PRO ASN ASN PRO LYS GLU CYS ASN LEU SEQRES 11 A 330 ILE GLU GLY GLU ASP HIS VAL GLU VAL ASN GLY GLU VAL SEQRES 12 A 330 PHE GLN LYS PRO PHE VAL GLU LYS PRO VAL SER ALA GLU SEQRES 13 A 330 ASP HIS ASN VAL TYR ILE TYR TYR PRO THR SER ALA GLY SEQRES 14 A 330 GLY GLY SER GLN ARG LEU PHE ARG LYS ILE GLY SER ARG SEQRES 15 A 330 SER SER VAL TYR SER PRO GLU SER ASN VAL ARG LYS THR SEQRES 16 A 330 GLY SER TYR ILE TYR GLU GLU PHE MET PRO THR ASP GLY SEQRES 17 A 330 THR ASP VAL LYS VAL TYR THR VAL GLY PRO ASP TYR ALA SEQRES 18 A 330 HIS ALA GLU ALA ARG LYS SER PRO ALA LEU ASP GLY LYS SEQRES 19 A 330 VAL GLU ARG ASP SER GLU GLY LYS GLU VAL ARG TYR PRO SEQRES 20 A 330 VAL ILE LEU ASN ALA ARG GLU LYS LEU ILE ALA TRP LYS SEQRES 21 A 330 VAL CYS LEU ALA PHE LYS GLN THR VAL CYS GLY PHE ASP SEQRES 22 A 330 LEU LEU ARG ALA ASN GLY GLN SER TYR VAL CYS ASP VAL SEQRES 23 A 330 ASN GLY PHE SER PHE VAL LYS ASN SER MET LYS TYR TYR SEQRES 24 A 330 ASP ASP CYS ALA LYS ILE LEU GLY ASN ILE VAL MET ARG SEQRES 25 A 330 GLU LEU ALA PRO GLN PHE HIS ILE PRO TRP SER ILE PRO SEQRES 26 A 330 LEU GLU ALA GLU ASP HET ADP A 401 27 HET I8P A 501 44 HET CD A 601 1 HET MG A 602 1 HET MG A 603 1 HET MG A 604 1 HET MG A 605 1 HET MG A 606 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM I8P (1R,3S,4R,5S,6R)-2,4,5,6-TETRAKIS(PHOSPHONOOXY) HETNAM 2 I8P CYCLOHEXANE-1,3-DIYL BIS[TRIHYDROGEN (DIPHOSPHATE)] HETNAM CD CADMIUM ION HETNAM MG MAGNESIUM ION HETSYN I8P 1D-MYO-INOSITOL 1,5-BISDIPHOSPHATE 2,3,4,6- HETSYN 2 I8P TETRAKISPHOSPHATE FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 I8P C6 H20 O30 P8 FORMUL 4 CD CD 2+ FORMUL 5 MG 5(MG 2+) FORMUL 10 HOH *400(H2 O) HELIX 1 1 MET A 51 LYS A 56 1 6 HELIX 2 2 SER A 57 SER A 68 1 12 HELIX 3 3 GLU A 79 GLU A 86 1 8 HELIX 4 4 PRO A 87 TRP A 91 5 5 HELIX 5 5 PRO A 106 ASN A 118 1 13 HELIX 6 6 ASN A 126 GLN A 132 1 7 HELIX 7 7 ASP A 133 GLU A 144 1 12 HELIX 8 8 PRO A 201 GLY A 205 5 5 HELIX 9 9 ASN A 287 LYS A 302 1 16 HELIX 10 10 SER A 331 ALA A 351 1 21 SHEET 1 A 4 ILE A 73 VAL A 77 0 SHEET 2 A 4 ILE A 44 CYS A 49 1 N VAL A 46 O THR A 74 SHEET 3 A 4 CYS A 96 SER A 99 1 O CYS A 96 N GLY A 47 SHEET 4 A 4 PHE A 120 VAL A 121 1 O PHE A 120 N LEU A 97 SHEET 1 B 6 TYR A 151 LEU A 154 0 SHEET 2 B 6 TYR A 234 GLU A 238 -1 O TYR A 234 N LEU A 154 SHEET 3 B 6 PHE A 184 PRO A 188 -1 N VAL A 185 O GLU A 237 SHEET 4 B 6 TYR A 197 TYR A 199 -1 O TYR A 197 N GLU A 186 SHEET 5 B 6 SER A 208 ILE A 215 -1 O GLN A 209 N ILE A 198 SHEET 6 B 6 ARG A 218 SER A 223 -1 O VAL A 221 N ARG A 210 SHEET 1 C 3 LEU A 166 GLU A 168 0 SHEET 2 C 3 HIS A 172 VAL A 175 -1 O GLU A 174 N ILE A 167 SHEET 3 C 3 GLU A 178 GLN A 181 -1 O PHE A 180 N VAL A 173 SHEET 1 D 5 TYR A 282 PRO A 283 0 SHEET 2 D 5 ALA A 257 LYS A 263 -1 N ALA A 261 O TYR A 282 SHEET 3 D 5 THR A 245 VAL A 252 -1 N LYS A 248 O GLU A 260 SHEET 4 D 5 VAL A 305 ALA A 313 -1 O PHE A 308 N VAL A 249 SHEET 5 D 5 GLN A 316 GLY A 324 -1 O GLY A 324 N GLY A 307 LINK O HOH A 22 MG MG A 602 1555 1555 2.14 LINK O SER A 68 MG MG A 603 1555 1555 2.37 LINK O PHE A 70 MG MG A 603 1555 1555 2.38 LINK O ILE A 73 MG MG A 603 1555 1555 2.12 LINK OG1 THR A 251 MG MG A 606 1555 1555 2.02 LINK O GLN A 303 MG MG A 606 1555 1555 2.23 LINK O THR A 304 MG MG A 606 1555 1555 2.61 LINK OD2 ASP A 309 MG MG A 602 1555 1555 2.00 LINK OD2 ASP A 321 CD CD A 601 1555 1555 2.36 LINK OD1 ASP A 321 CD CD A 601 1555 1555 2.61 LINK OD2 ASP A 321 MG MG A 602 1555 1555 2.14 LINK OD1 ASN A 323 CD CD A 601 1555 1555 2.24 LINK O HOH A 369 MG MG A 604 1555 1555 2.15 LINK O HOH A 399 CD CD A 601 1555 1555 2.09 LINK O2B ADP A 401 CD CD A 601 1555 1555 2.21 LINK O3B ADP A 401 MG MG A 602 1555 1555 2.08 LINK O2A ADP A 401 MG MG A 602 1555 1555 2.10 LINK O HOH A 480 MG MG A 605 1555 1555 2.35 LINK O HOH A 483 MG MG A 605 1555 1555 2.27 LINK O51 I8P A 501 CD CD A 601 1555 1555 2.09 LINK O61 I8P A 501 MG MG A 602 1555 1555 2.22 LINK O35 I8P A 501 MG MG A 604 1555 1555 2.08 LINK O44 I8P A 501 MG MG A 604 1555 1555 2.15 LINK O HOH A 508 MG MG A 603 1555 1555 2.77 LINK O HOH A 517 MG MG A 605 1555 1555 2.05 LINK O HOH A 524 MG MG A 605 1555 1555 2.20 LINK O HOH A 534 MG MG A 604 1555 1555 2.17 LINK O HOH A 549 MG MG A 604 1555 1555 2.12 LINK O HOH A 556 MG MG A 603 1555 1555 2.34 LINK O HOH A 599 MG MG A 605 1555 1555 2.17 LINK MG MG A 604 O HOH A 610 1555 1555 2.04 LINK MG MG A 605 O HOH A 700 1555 1555 2.36 CISPEP 1 LYS A 182 PRO A 183 0 3.70 SITE 1 AC1 24 HOH A 22 ARG A 134 PRO A 149 VAL A 185 SITE 2 AC1 24 LYS A 187 HIS A 194 LEU A 211 GLU A 237 SITE 3 AC1 24 GLU A 238 PHE A 239 MET A 240 ASP A 246 SITE 4 AC1 24 PRO A 265 ASP A 309 LEU A 311 CYS A 320 SITE 5 AC1 24 ASP A 321 HOH A 368 HOH A 406 HOH A 413 SITE 6 AC1 24 HOH A 447 I8P A 501 CD A 601 MG A 602 SITE 1 AC2 45 LYS A 53 LYS A 54 HIS A 194 ARG A 213 SITE 2 AC2 45 LYS A 214 LYS A 248 ARG A 262 ARG A 273 SITE 3 AC2 45 ARG A 281 ASP A 309 ASP A 321 ASN A 323 SITE 4 AC2 45 SER A 326 LYS A 329 HOH A 369 ADP A 401 SITE 5 AC2 45 HOH A 416 HOH A 447 HOH A 450 HOH A 524 SITE 6 AC2 45 HOH A 534 HOH A 538 HOH A 549 HOH A 555 SITE 7 AC2 45 HOH A 580 HOH A 594 CD A 601 MG A 602 SITE 8 AC2 45 MG A 604 HOH A 610 HOH A 614 HOH A 615 SITE 9 AC2 45 HOH A 619 HOH A 622 HOH A 631 HOH A 649 SITE 10 AC2 45 HOH A 650 HOH A 656 HOH A 674 HOH A 681 SITE 11 AC2 45 HOH A 683 HOH A 698 HOH A 709 HOH A 711 SITE 12 AC2 45 HOH A 716 SITE 1 AC3 5 ASP A 321 ASN A 323 HOH A 399 ADP A 401 SITE 2 AC3 5 I8P A 501 SITE 1 AC4 5 HOH A 22 ASP A 309 ASP A 321 ADP A 401 SITE 2 AC4 5 I8P A 501 SITE 1 AC5 5 SER A 68 PHE A 70 ILE A 73 HOH A 508 SITE 2 AC5 5 HOH A 556 SITE 1 AC6 5 HOH A 369 I8P A 501 HOH A 534 HOH A 549 SITE 2 AC6 5 HOH A 610 SITE 1 AC7 7 ASN A 323 HOH A 480 HOH A 483 HOH A 517 SITE 2 AC7 7 HOH A 524 HOH A 599 HOH A 700 SITE 1 AC8 5 THR A 251 CYS A 298 GLN A 303 THR A 304 SITE 2 AC8 5 CYS A 306 CRYST1 89.036 110.009 41.484 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 0.011231 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009090 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024106 0.00000