HEADER TRANSFERASE 14-APR-14 4Q4D TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN DIPHOSPHOINOSITOL TITLE 2 PENTAKISPHOSPHATE KINASE 2 (PPIP5K2) IN COMPLEX WITH AMP-PNP AND TITLE 3 SYNTHETIC 3,5-(PP)2-IP4 (3,5-IP8) COMPND MOL_ID: 1; COMPND 2 MOLECULE: INOSITOL HEXAKISPHOSPHATE AND DIPHOSPHOINOSITOL- COMPND 3 PENTAKISPHOSPHATE KINASE 2; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: KINASE DOMAIN (UNP RESIDUES 41-366); 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: PPIP5K2, HISPPD1, KIAA0433, VIP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ARCTICEXPRESS (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST566 KEYWDS KINASE, SYNTHESIS, INOSITOL PYROPHOSPHATE, ENANTIOMER, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,S.B.SHEARS REVDAT 3 20-SEP-23 4Q4D 1 REMARK SEQADV LINK REVDAT 2 10-SEP-14 4Q4D 1 JRNL REVDAT 1 06-AUG-14 4Q4D 0 JRNL AUTH S.CAPOLICCHIO,H.WANG,D.T.THAKOR,S.B.SHEARS,H.J.JESSEN JRNL TITL SYNTHESIS OF DENSELY PHOSPHORYLATED JRNL TITL 2 BIS-1,5-DIPHOSPHO-MYO-INOSITOL TETRAKISPHOSPHATE AND ITS JRNL TITL 3 ENANTIOMER BY BIDIRECTIONAL P-ANHYDRIDE FORMATION. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 53 9508 2014 JRNL REFN ISSN 1433-7851 JRNL PMID 25044992 JRNL DOI 10.1002/ANIE.201404398 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 33431 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 RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2197 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2295 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE SET COUNT : 165 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2539 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 403 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32000 REMARK 3 B22 (A**2) : -0.23000 REMARK 3 B33 (A**2) : -0.09000 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): 0.130 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.124 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.662 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2747 ; 0.010 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2556 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3748 ; 1.580 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5911 ; 0.750 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 331 ; 5.531 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 126 ;37.625 ;24.048 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 472 ;13.080 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.238 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 406 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3063 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 620 ; 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): 1306 ; 1.003 ; 1.218 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1304 ; 1.002 ; 1.216 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1643 ; 1.688 ; 1.820 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1644 ; 1.688 ; 1.821 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1441 ; 1.511 ; 1.483 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1433 ; 1.503 ; 1.468 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2093 ; 2.445 ; 2.144 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3455 ; 6.686 ;12.197 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3229 ; 6.286 ;10.994 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 43 A 359 REMARK 3 RESIDUE RANGE : A 401 A 405 REMARK 3 ORIGIN FOR THE GROUP (A): -0.3561 15.2105 3.6185 REMARK 3 T TENSOR REMARK 3 T11: 0.0133 T22: 0.0107 REMARK 3 T33: 0.0072 T12: -0.0056 REMARK 3 T13: 0.0007 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.4805 L22: 0.7468 REMARK 3 L33: 0.6506 L12: -0.2732 REMARK 3 L13: 0.0826 L23: -0.2915 REMARK 3 S TENSOR REMARK 3 S11: 0.0151 S12: 0.0082 S13: -0.0111 REMARK 3 S21: -0.0073 S22: 0.0220 S23: 0.0579 REMARK 3 S31: 0.0272 S32: -0.0184 S33: -0.0371 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: NULL REMARK 4 REMARK 4 4Q4D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000085588. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : 35810 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 25.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36600 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 3T9F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% W/V PEG3350, 20 MM MAGNESIUM REMARK 280 CHLORIDE, 0.1 M HEPES, PH 7.0, 1 MM AMP-PNP, 2 MM CADMIUM REMARK 280 CHLORIDE, CRYSTALS TRANSFERRED TO STABILIZING BUFFER (22% W/V REMARK 280 PEG3350, 10 MM MAGNESIUM CHLORIDE, 0.1 M SODIUM ACETATE, PH 5.2) REMARK 280 AT 277 K OVERNIGHT (ATP IN THE CRYSTALS WAS HYDROLYZED TO ADP) REMARK 280 THEN SOAKED FOR THREE DAYS IN STABILIZING BUFFER CONTAINING 2 MM REMARK 280 3,5-IP8, VAPOR DIFFUSION, HANGING DROP 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 44.39500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.68950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.34050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.68950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.39500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.34050 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 ILE A 360 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: 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 321 136.47 -171.20 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 90.2 REMARK 620 3 ILE A 73 O 125.2 93.4 REMARK 620 4 HOH A 637 O 82.6 88.8 152.0 REMARK 620 5 HOH A 678 O 91.1 178.7 85.6 91.5 REMARK 620 6 HOH A 766 O 144.3 102.0 87.8 64.4 77.0 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 96.8 REMARK 620 3 ANP A 401 O1G 108.5 84.8 REMARK 620 4 ANP A 401 O2A 114.8 94.1 136.5 REMARK 620 5 HOH A 522 O 87.3 175.9 93.3 84.8 REMARK 620 N 1 2 3 4 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 56.5 REMARK 620 3 ASN A 323 OD1 87.1 90.2 REMARK 620 4 ANP A 401 O3G 97.0 153.1 93.1 REMARK 620 5 ANP A 401 O1B 81.0 85.2 167.9 86.1 REMARK 620 6 HOH A 819 O 157.1 100.6 93.7 105.8 98.1 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 2YN 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Q4C RELATED DB: PDB DBREF 4Q4D A 41 366 UNP O43314 VIP2_HUMAN 41 366 SEQADV 4Q4D GLY A 37 UNP O43314 EXPRESSION TAG SEQADV 4Q4D SER A 38 UNP O43314 EXPRESSION TAG SEQADV 4Q4D PHE A 39 UNP O43314 EXPRESSION TAG SEQADV 4Q4D 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 2YN A 402 44 HET MG A 403 1 HET MG A 404 1 HET MG A 405 1 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM 2YN (1R,3S,4S,5R,6S)-2,4,5,6-TETRAKIS(PHOSPHONOOXY) HETNAM 2 2YN CYCLOHEXANE-1,3-DIYL BIS[TRIHYDROGEN (DIPHOSPHATE)] HETNAM MG MAGNESIUM ION FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 2YN C6 H20 O30 P8 FORMUL 4 MG 3(MG 2+) FORMUL 7 HOH *403(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 HIS A 355 1 25 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 SER A 223 N SER A 208 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 SER A 68 MG MG A 405 1555 1555 2.35 LINK O PHE A 70 MG MG A 405 1555 1555 2.42 LINK O ILE A 73 MG MG A 405 1555 1555 2.27 LINK OD2 ASP A 309 MG MG A 404 1555 1555 1.94 LINK OD2 ASP A 321 MG MG A 403 1555 1555 2.16 LINK OD1 ASP A 321 MG MG A 403 1555 1555 2.42 LINK OD2 ASP A 321 MG MG A 404 1555 1555 2.28 LINK OD1 ASN A 323 MG MG A 403 1555 1555 2.10 LINK O3G ANP A 401 MG MG A 403 1555 1555 1.98 LINK O1B ANP A 401 MG MG A 403 1555 1555 2.14 LINK O1G ANP A 401 MG MG A 404 1555 1555 1.96 LINK O2A ANP A 401 MG MG A 404 1555 1555 2.08 LINK MG MG A 403 O HOH A 819 1555 1555 1.75 LINK MG MG A 404 O HOH A 522 1555 1555 2.13 LINK MG MG A 405 O HOH A 637 1555 1555 2.49 LINK MG MG A 405 O HOH A 678 1555 1555 2.33 LINK MG MG A 405 O HOH A 766 1555 1555 2.40 CISPEP 1 LYS A 182 PRO A 183 0 3.28 SITE 1 AC1 26 ARG A 134 PRO A 149 LYS A 187 HIS A 194 SITE 2 AC1 26 LEU A 211 GLU A 237 GLU A 238 PHE A 239 SITE 3 AC1 26 MET A 240 ASP A 246 LYS A 248 SER A 264 SITE 4 AC1 26 ASP A 309 LEU A 311 CYS A 320 ASP A 321 SITE 5 AC1 26 ASN A 323 MG A 403 MG A 404 HOH A 522 SITE 6 AC1 26 HOH A 540 HOH A 547 HOH A 580 HOH A 709 SITE 7 AC1 26 HOH A 819 HOH A 846 SITE 1 AC2 24 LYS A 53 LYS A 54 SER A 102 LYS A 103 SITE 2 AC2 24 LYS A 214 LYS A 248 TYR A 250 ARG A 262 SITE 3 AC2 24 ARG A 273 ARG A 281 SER A 326 LYS A 329 SITE 4 AC2 24 HOH A 612 HOH A 615 HOH A 650 HOH A 677 SITE 5 AC2 24 HOH A 709 HOH A 711 HOH A 716 HOH A 720 SITE 6 AC2 24 HOH A 726 HOH A 787 HOH A 820 HOH A 882 SITE 1 AC3 4 ASP A 321 ASN A 323 ANP A 401 HOH A 819 SITE 1 AC4 4 ASP A 309 ASP A 321 ANP A 401 HOH A 522 SITE 1 AC5 6 SER A 68 PHE A 70 ILE A 73 HOH A 637 SITE 2 AC5 6 HOH A 678 HOH A 766 CRYST1 88.790 110.681 41.379 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 0.011263 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009035 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024167 0.00000