HEADER TRANSFERASE/TRANSFERASE INHIBITOR 18-OCT-12 4HN2 TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN DIPHOSPHOINOSITOL TITLE 2 PENTAKISPHOSPHATE KINASE 2 (PPIP5K2) IN COMPLEX WITH AMPPNP AND A TITLE 3 SUBSTRATE ANALOG 5PA-IP5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INOSITOL HEXAKISPHOSPHATE AND DIPHOSPHOINOSITOL- COMPND 3 PENTAKISPHOSPHATE KINASE 2; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: ATP-GRASP KINASE DOMAIN; COMPND 6 SYNONYM: DIPHOSPHOINOSITOL PENTAKISPHOSPHATE KINASE 2, HISTIDINE ACID COMPND 7 PHOSPHATASE DOMAIN-CONTAINING PROTEIN 1, INSP6 AND PP-IP5 KINASE 2, COMPND 8 VIP1 HOMOLOG 2, HSVIP2; COMPND 9 EC: 2.7.4.21, 2.7.4.24; COMPND 10 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: HISPPD1, KIAA0433, PPIP5K2, VIP2; 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, PYROPHOSPHATE ANALOG, TRANSFERASE-TRANSFERASE INHIBITOR KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG REVDAT 3 20-SEP-23 4HN2 1 REMARK SEQADV LINK REVDAT 2 07-NOV-12 4HN2 1 JRNL REVDAT 1 31-OCT-12 4HN2 0 SPRSDE 31-OCT-12 4HN2 4GB4 JRNL AUTH A.M.RILEY,H.WANG,J.D.WEAVER,S.B.SHEARS,B.V.POTTER JRNL TITL FIRST SYNTHETIC ANALOGUES OF DIPHOSPHOINOSITOL JRNL TITL 2 POLYPHOSPHATES: INTERACTION WITH PP-INSP(5) KINASE. JRNL REF CHEM.COMMUN.(CAMB.) V. 48 11292 2012 JRNL REFN ISSN 1359-7345 JRNL PMID 23032903 JRNL DOI 10.1039/C2CC36044F REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 30868 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2011 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2235 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 140 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2604 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.65000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : -0.42000 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): 0.153 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.137 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.787 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2836 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3872 ; 1.249 ; 2.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 348 ; 5.179 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;36.154 ;24.060 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 497 ;12.680 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;15.052 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 419 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2149 ; 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): 1679 ; 0.713 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2743 ; 1.399 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1157 ; 2.052 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1123 ; 3.489 ; 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 4HN2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075670. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-12 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 : 33091 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 98.3 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 FOR THE DATA SET : 24.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38600 REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.5.0109 REMARK 200 STARTING MODEL: PDB ENTRY 3T9B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 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 AMPPNP, 2 MM CDCL2. SOAKING WITH 2 MM 5-PA- REMARK 280 INSP5 UNDER PH 5.2 FOR 3 DAYS, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 44.83300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.76800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.38400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.76800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.83300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.38400 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 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 -12.86 -146.30 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 405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 68 O REMARK 620 2 PHE A 70 O 93.7 REMARK 620 3 ILE A 73 O 125.1 95.5 REMARK 620 4 HOH A 657 O 85.4 178.7 85.8 REMARK 620 5 HOH A 695 O 136.1 109.9 89.9 70.3 REMARK 620 6 HOH A 777 O 78.9 88.8 155.0 90.1 65.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 309 OD2 REMARK 620 2 ASP A 321 OD2 101.3 REMARK 620 3 ANP A 401 O2A 107.4 93.0 REMARK 620 4 ANP A 401 O1G 110.7 92.2 139.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 321 OD2 REMARK 620 2 ASP A 321 OD1 53.3 REMARK 620 3 ANP A 401 O3G 90.9 144.2 REMARK 620 4 ANP A 401 O2B 79.2 88.0 86.7 REMARK 620 5 HOH A 738 O 157.5 104.9 110.5 108.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 406 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 560 O REMARK 620 2 HOH A 573 O 90.0 REMARK 620 3 HOH A 628 O 83.4 84.4 REMARK 620 4 HOH A 653 O 87.3 92.1 170.1 REMARK 620 5 HOH A 686 O 87.9 165.4 80.9 102.3 REMARK 620 6 HOH A 776 O 163.3 106.4 95.1 94.7 75.5 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 ANP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0EJ A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3T9D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN REMARK 900 DIPHOSPHOINOSITOL PENTAKISPHOSPHATE KINASE 2 (PPIP5K2) IN COMPLEX REMARK 900 WITH AMPPNP AND 5-(PP)-IP5 (5-IP7) REMARK 900 RELATED ID: 3T9B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN REMARK 900 DIPHOSPHOINOSITOL PENTAKISPHOSPHATE KINASE 2 (PPIP5K2) IN COMPLEX REMARK 900 WITH AMPPNP AT PH 5.2 DBREF 4HN2 A 41 366 UNP O43314 VIP2_HUMAN 41 366 SEQADV 4HN2 GLY A 37 UNP O43314 EXPRESSION TAG SEQADV 4HN2 SER A 38 UNP O43314 EXPRESSION TAG SEQADV 4HN2 PHE A 39 UNP O43314 EXPRESSION TAG SEQADV 4HN2 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 ANP A 401 31 HET 0EJ A 402 39 HET MG A 403 1 HET MG A 404 1 HET MG A 405 1 HET MG A 406 1 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM 0EJ (2-OXO-2-{[(1S,2R,3S,4S,5R,6S)-2,3,4,5,6- HETNAM 2 0EJ PENTAKIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}ETHYL)PHOSPHONIC HETNAM 3 0EJ ACID HETNAM MG MAGNESIUM ION FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 0EJ C8 H20 O25 P6 FORMUL 4 MG 4(MG 2+) FORMUL 8 HOH *330(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 ILE A 131 1 6 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 ILE A 98 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 LYS A 187 O ILE A 235 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 GLU A 178 N VAL A 175 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 TYR A 318 N LEU A 311 LINK O SER A 68 MG MG A 405 1555 1555 2.30 LINK O PHE A 70 MG MG A 405 1555 1555 2.33 LINK O ILE A 73 MG MG A 405 1555 1555 2.26 LINK OD2 ASP A 309 MG MG A 404 1555 1555 1.80 LINK OD2 ASP A 321 MG MG A 403 1555 1555 2.13 LINK OD1 ASP A 321 MG MG A 403 1555 1555 2.63 LINK OD2 ASP A 321 MG MG A 404 1555 1555 2.41 LINK O3G ANP A 401 MG MG A 403 1555 1555 1.94 LINK O2B ANP A 401 MG MG A 403 1555 1555 2.13 LINK O2A ANP A 401 MG MG A 404 1555 1555 1.99 LINK O1G ANP A 401 MG MG A 404 1555 1555 2.09 LINK MG MG A 403 O HOH A 738 1555 1555 1.83 LINK MG MG A 405 O HOH A 657 1555 1555 2.38 LINK MG MG A 405 O HOH A 695 1555 1555 2.31 LINK MG MG A 405 O HOH A 777 1555 1555 2.64 LINK MG MG A 406 O HOH A 560 1555 1555 2.35 LINK MG MG A 406 O HOH A 573 1555 1555 2.18 LINK MG MG A 406 O HOH A 628 1555 1555 2.12 LINK MG MG A 406 O HOH A 653 1555 1555 2.21 LINK MG MG A 406 O HOH A 686 1555 1555 2.10 LINK MG MG A 406 O HOH A 776 1555 1555 2.28 CISPEP 1 LYS A 182 PRO A 183 0 2.27 SITE 1 AC1 27 ARG A 134 PRO A 149 LYS A 187 HIS A 194 SITE 2 AC1 27 LEU A 211 ARG A 213 GLU A 237 GLU A 238 SITE 3 AC1 27 PHE A 239 MET A 240 ASP A 246 LYS A 248 SITE 4 AC1 27 ARG A 262 SER A 264 ASP A 309 LEU A 311 SITE 5 AC1 27 CYS A 320 ASP A 321 ASN A 323 0EJ A 402 SITE 6 AC1 27 MG A 403 MG A 404 HOH A 571 HOH A 579 SITE 7 AC1 27 HOH A 737 HOH A 738 HOH A 778 SITE 1 AC2 21 LYS A 53 LYS A 54 ARG A 213 LYS A 214 SITE 2 AC2 21 LYS A 248 ARG A 281 SER A 326 LYS A 329 SITE 3 AC2 21 ANP A 401 HOH A 557 HOH A 573 HOH A 575 SITE 4 AC2 21 HOH A 592 HOH A 593 HOH A 613 HOH A 648 SITE 5 AC2 21 HOH A 653 HOH A 712 HOH A 729 HOH A 737 SITE 6 AC2 21 HOH A 830 SITE 1 AC3 4 ASP A 321 ASN A 323 ANP A 401 HOH A 738 SITE 1 AC4 3 ASP A 309 ASP A 321 ANP A 401 SITE 1 AC5 6 SER A 68 PHE A 70 ILE A 73 HOH A 657 SITE 2 AC5 6 HOH A 695 HOH A 777 SITE 1 AC6 6 HOH A 560 HOH A 573 HOH A 628 HOH A 653 SITE 2 AC6 6 HOH A 686 HOH A 776 CRYST1 89.666 110.768 41.536 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 0.011152 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024076 0.00000