HEADER TRANSFERASE 27-AUG-15 5DGH TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN DIPHOSPHOINOSITOL TITLE 2 PENTAKISPHOSPHATE KINASE 2 (PPIP5K2) IN COMPLEX WITH AMP-PNP AND 5- TITLE 3 (PCP)-IP5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INOSITOL HEXAKISPHOSPHATE AND DIPHOSPHOINOSITOL- COMPND 3 PENTAKISPHOSPHATE KINASE 2; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: DIPHOSPHOINOSITOL PENTAKISPHOSPHATE KINASE 2,HISTIDINE ACID COMPND 6 PHOSPHATASE DOMAIN-CONTAINING PROTEIN 1,INSP6 AND PP-IP5 KINASE 2, COMPND 7 VIP1 HOMOLOG 2,HSVIP2; COMPND 8 EC: 2.7.4.21,2.7.4.24; COMPND 9 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: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 ARCTIC EXPRESS (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST566 KEYWDS TRANSFERASE INOSITOL DIPHOSPHOINOSITOL PENTAKISPHOSPHATE KINASE KEYWDS 2 ANALOG METHYLENEBISPHOSPHONATE PPIP5K ATP-GRASP PYROPHOSPHATE KEYWDS 3 DIPHOSPHATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,S.B.SHEARS REVDAT 5 27-SEP-23 5DGH 1 LINK REVDAT 4 18-DEC-19 5DGH 1 REMARK REVDAT 3 20-SEP-17 5DGH 1 REMARK REVDAT 2 24-AUG-16 5DGH 1 JRNL REVDAT 1 10-AUG-16 5DGH 0 JRNL AUTH A.HAGER,M.WU,H.WANG,N.W.BROWN,S.B.SHEARS,N.VEIGA,D.FIEDLER JRNL TITL CELLULAR CATIONS CONTROL CONFORMATIONAL SWITCHING OF JRNL TITL 2 INOSITOL PYROPHOSPHATE ANALOGUES. JRNL REF CHEMISTRY V. 22 12406 2016 JRNL REFN ISSN 0947-6539 JRNL PMID 27460418 JRNL DOI 10.1002/CHEM.201601754 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 21891 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1429 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1425 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 100 REMARK 3 BIN FREE R VALUE : 0.3030 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 : 108 REMARK 3 SOLVENT ATOMS : 266 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.31000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : -0.30000 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): 0.218 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.184 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.275 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2722 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3681 ; 1.450 ; 2.002 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 320 ; 5.761 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;36.917 ;24.228 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 462 ;14.047 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;11.566 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 399 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2017 ; 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): 1279 ; 1.590 ; 2.259 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1598 ; 2.791 ; 3.376 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1443 ; 1.751 ; 2.460 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4407 ; 6.328 ;19.752 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 : 1.20 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 5DGH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000213049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM 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 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23365 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.38200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3T7A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 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 AMP-PNP AND 2 MM CDCL2. THE CRYSTALS WERE REMARK 280 TRANSFERRED TO A STABILIZING BUFFER CONTAINING 22% (W/V) PEG REMARK 280 3350, 10 MM MGCL2, 0.1 M SODIUM ACETATE, PH 5.2 AT 4 OC REMARK 280 OVERNIGHT. THE CRYSTALS WERE SOAKED UNDER THE ABOVE STABILIZING REMARK 280 BUFFER FOR THREE DAYS WITH 2 MM COMPOUND., VAPOR DIFFUSION, REMARK 280 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 43.95000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.62650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.17000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.62650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.95000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.17000 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 LYS A 162 72.66 -67.14 REMARK 500 ASN A 165 45.03 -86.29 REMARK 500 LYS A 214 123.99 -24.42 REMARK 500 LEU A 267 -105.91 -69.85 REMARK 500 ASP A 321 130.79 -171.38 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 96.0 REMARK 620 3 ILE A 73 O 123.5 99.8 REMARK 620 4 HOH A 540 O 147.6 101.8 80.0 REMARK 620 5 HOH A 654 O 76.9 87.8 156.7 76.9 REMARK 620 6 HOH A 701 O 85.5 176.1 82.2 75.2 89.0 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 90.8 REMARK 620 3 ANP A 401 O1G 104.0 89.5 REMARK 620 4 ANP A 401 O2A 113.4 90.4 142.6 REMARK 620 5 HOH A 574 O 88.9 179.1 89.7 90.5 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 OD1 REMARK 620 2 ASP A 321 OD2 59.0 REMARK 620 3 ASN A 323 OD1 88.1 90.5 REMARK 620 4 ANP A 401 O3G 149.0 90.8 85.1 REMARK 620 5 ANP A 401 O1B 92.7 82.0 170.7 89.5 REMARK 620 6 HOH A 563 O 104.4 163.4 89.0 105.6 99.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 407 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 5A3 A 402 O35 REMARK 620 2 5A3 A 402 O44 82.8 REMARK 620 3 HOH A 559 O 99.3 89.2 REMARK 620 4 HOH A 568 O 65.3 80.4 162.3 REMARK 620 5 HOH A 651 O 90.6 172.8 94.7 94.2 REMARK 620 6 HOH A 728 O 174.1 96.3 86.5 108.8 89.9 REMARK 620 N 1 2 3 4 5 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 506 O REMARK 620 2 HOH A 520 O 89.7 REMARK 620 3 HOH A 571 O 74.2 163.7 REMARK 620 4 HOH A 587 O 176.3 90.1 106.2 REMARK 620 5 HOH A 697 O 82.1 87.9 87.3 101.5 REMARK 620 6 HOH A 731 O 84.9 91.7 89.5 91.4 167.0 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 5A3 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 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 415 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DGI RELATED DB: PDB DBREF 5DGH A 41 366 UNP O43314 VIP2_HUMAN 41 366 SEQADV 5DGH GLY A 37 UNP O43314 EXPRESSION TAG SEQADV 5DGH SER A 38 UNP O43314 EXPRESSION TAG SEQADV 5DGH PHE A 39 UNP O43314 EXPRESSION TAG SEQADV 5DGH 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 5A3 A 402 40 HET MG A 403 1 HET MG A 404 1 HET MG A 405 1 HET MG A 406 1 HET MG A 407 1 HET EDO A 408 4 HET ACT A 409 4 HET EDO A 410 4 HET EDO A 411 4 HET EDO A 412 4 HET ACT A 413 4 HET EDO A 414 4 HET EDO A 415 4 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM 5A3 METHYLENEBISPHOSPHONATE INOSITOL PENTAKISPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM ACT ACETATE ION HETSYN 5A3 {[(R)-HYDROXY{[(1S,2R,3S,4S,5R,6S)-2,3,4,5,6- HETSYN 2 5A3 PENTAKIS(PHOSPHONOOXY) HETSYN 3 5A3 CYCLOHEXYL]OXY}PHOSPHORYL]METHYL}PHOSPHONIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 5A3 C7 H21 O26 P7 FORMUL 4 MG 5(MG 2+) FORMUL 9 EDO 6(C2 H6 O2) FORMUL 10 ACT 2(C2 H3 O2 1-) FORMUL 17 HOH *266(H2 O) HELIX 1 AA1 MET A 51 LYS A 56 1 6 HELIX 2 AA2 SER A 57 SER A 68 1 12 HELIX 3 AA3 GLU A 79 GLU A 86 1 8 HELIX 4 AA4 PRO A 87 TRP A 91 5 5 HELIX 5 AA5 PRO A 106 ASN A 118 1 13 HELIX 6 AA6 ASN A 126 GLN A 132 1 7 HELIX 7 AA7 ASP A 133 GLU A 144 1 12 HELIX 8 AA8 PRO A 201 GLY A 205 5 5 HELIX 9 AA9 ASN A 287 LYS A 302 1 16 HELIX 10 AB1 SER A 331 ALA A 351 1 21 SHEET 1 AA1 4 ILE A 73 VAL A 77 0 SHEET 2 AA1 4 ILE A 44 CYS A 49 1 N ILE A 48 O VAL A 76 SHEET 3 AA1 4 CYS A 96 SER A 99 1 O CYS A 96 N GLY A 47 SHEET 4 AA1 4 PHE A 120 VAL A 121 1 O PHE A 120 N LEU A 97 SHEET 1 AA2 6 TYR A 151 LEU A 154 0 SHEET 2 AA2 6 TYR A 234 GLU A 238 -1 O TYR A 234 N LEU A 154 SHEET 3 AA2 6 PHE A 184 PRO A 188 -1 N VAL A 185 O GLU A 237 SHEET 4 AA2 6 TYR A 197 TYR A 199 -1 O TYR A 197 N GLU A 186 SHEET 5 AA2 6 SER A 208 ILE A 215 -1 O GLN A 209 N ILE A 198 SHEET 6 AA2 6 ARG A 218 SER A 223 -1 O SER A 223 N SER A 208 SHEET 1 AA3 3 LEU A 166 GLU A 168 0 SHEET 2 AA3 3 HIS A 172 VAL A 175 -1 O GLU A 174 N ILE A 167 SHEET 3 AA3 3 GLU A 178 GLN A 181 -1 O GLU A 178 N VAL A 175 SHEET 1 AA4 5 TYR A 282 PRO A 283 0 SHEET 2 AA4 5 ALA A 257 LYS A 263 -1 N ALA A 261 O TYR A 282 SHEET 3 AA4 5 THR A 245 VAL A 252 -1 N LYS A 248 O GLU A 260 SHEET 4 AA4 5 VAL A 305 ALA A 313 -1 O PHE A 308 N VAL A 249 SHEET 5 AA4 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 2.19 LINK O PHE A 70 MG MG A 405 1555 1555 2.20 LINK O ILE A 73 MG MG A 405 1555 1555 2.20 LINK OD2 ASP A 309 MG MG A 404 1555 1555 2.13 LINK OD1 ASP A 321 MG MG A 403 1555 1555 2.19 LINK OD2 ASP A 321 MG MG A 403 1555 1555 2.17 LINK OD2 ASP A 321 MG MG A 404 1555 1555 2.16 LINK OD1 ASN A 323 MG MG A 403 1555 1555 2.16 LINK O3G ANP A 401 MG MG A 403 1555 1555 2.06 LINK O1B ANP A 401 MG MG A 403 1555 1555 2.03 LINK O1G ANP A 401 MG MG A 404 1555 1555 1.99 LINK O2A ANP A 401 MG MG A 404 1555 1555 1.96 LINK O35 5A3 A 402 MG MG A 407 1555 1555 2.08 LINK O44 5A3 A 402 MG MG A 407 1555 1555 2.23 LINK MG MG A 403 O HOH A 563 1555 1555 1.93 LINK MG MG A 404 O HOH A 574 1555 1555 2.00 LINK MG MG A 405 O HOH A 540 1555 1555 2.34 LINK MG MG A 405 O HOH A 654 1555 1555 2.49 LINK MG MG A 405 O HOH A 701 1555 1555 2.50 LINK MG MG A 406 O HOH A 506 1555 1555 2.45 LINK MG MG A 406 O HOH A 520 1555 1555 2.22 LINK MG MG A 406 O HOH A 571 1555 1555 2.33 LINK MG MG A 406 O HOH A 587 1555 1555 2.36 LINK MG MG A 406 O HOH A 697 1555 1555 2.26 LINK MG MG A 406 O HOH A 731 1555 1555 2.14 LINK MG MG A 407 O HOH A 559 1555 1555 2.07 LINK MG MG A 407 O HOH A 568 1555 1555 2.83 LINK MG MG A 407 O HOH A 651 1555 1555 2.01 LINK MG MG A 407 O HOH A 728 1555 1555 2.34 CISPEP 1 LYS A 182 PRO A 183 0 5.39 SITE 1 AC1 26 ARG A 134 PRO A 149 VAL A 185 LYS A 187 SITE 2 AC1 26 HIS A 194 LEU A 211 ARG A 213 GLU A 237 SITE 3 AC1 26 GLU A 238 PHE A 239 MET A 240 ASP A 246 SITE 4 AC1 26 SER A 264 ASP A 309 LEU A 311 CYS A 320 SITE 5 AC1 26 ASP A 321 ASN A 323 MG A 403 MG A 404 SITE 6 AC1 26 HOH A 501 HOH A 533 HOH A 563 HOH A 574 SITE 7 AC1 26 HOH A 637 HOH A 685 SITE 1 AC2 25 LYS A 53 LYS A 54 ARG A 213 LYS A 214 SITE 2 AC2 25 LYS A 248 TYR A 250 ARG A 262 ARG A 273 SITE 3 AC2 25 SER A 326 LYS A 329 MG A 407 EDO A 410 SITE 4 AC2 25 HOH A 501 HOH A 506 HOH A 519 HOH A 557 SITE 5 AC2 25 HOH A 559 HOH A 568 HOH A 579 HOH A 580 SITE 6 AC2 25 HOH A 583 HOH A 585 HOH A 605 HOH A 608 SITE 7 AC2 25 HOH A 651 SITE 1 AC3 4 ASP A 321 ASN A 323 ANP A 401 HOH A 563 SITE 1 AC4 4 ASP A 309 ASP A 321 ANP A 401 HOH A 574 SITE 1 AC5 6 SER A 68 PHE A 70 ILE A 73 HOH A 540 SITE 2 AC5 6 HOH A 654 HOH A 701 SITE 1 AC6 6 HOH A 506 HOH A 520 HOH A 571 HOH A 587 SITE 2 AC6 6 HOH A 697 HOH A 731 SITE 1 AC7 5 5A3 A 402 HOH A 559 HOH A 568 HOH A 651 SITE 2 AC7 5 HOH A 728 SITE 1 AC8 5 ASN A 90 TRP A 91 PRO A 92 ILE A 285 SITE 2 AC8 5 HOH A 617 SITE 1 AC9 5 SER A 217 ARG A 218 LYS A 270 LEU A 292 SITE 2 AC9 5 HOH A 588 SITE 1 AD1 9 LYS A 248 VAL A 249 TYR A 250 GLY A 307 SITE 2 AD1 9 PHE A 308 ASP A 309 ASN A 323 SER A 326 SITE 3 AD1 9 5A3 A 402 SITE 1 AD2 5 ARG A 312 GLY A 315 GLN A 316 SER A 317 SITE 2 AD2 5 HOH A 525 SITE 1 AD3 7 PRO A 87 GLU A 89 ASN A 90 TYR A 256 SITE 2 AD3 7 HIS A 258 TYR A 334 HOH A 670 SITE 1 AD4 1 HOH A 620 SITE 1 AD5 6 PHE A 105 PRO A 106 LEU A 107 ASP A 108 SITE 2 AD5 6 HOH A 517 HOH A 621 SITE 1 AD6 5 VAL A 121 ASP A 124 LEU A 125 ASN A 126 SITE 2 AD6 5 HOH A 537 CRYST1 87.900 110.340 41.253 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 0.011377 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024241 0.00000 CONECT 197 2631 CONECT 211 2631 CONECT 243 2631 CONECT 2146 2630 CONECT 2237 2629 CONECT 2238 2629 2630 CONECT 2252 2629 CONECT 2558 2559 2560 2561 2565 CONECT 2559 2558 2630 CONECT 2560 2558 CONECT 2561 2558 2629 CONECT 2562 2563 2564 2565 2569 CONECT 2563 2562 2629 CONECT 2564 2562 CONECT 2565 2558 2562 CONECT 2566 2567 2568 2569 2570 CONECT 2567 2566 CONECT 2568 2566 2630 CONECT 2569 2562 2566 CONECT 2570 2566 2571 CONECT 2571 2570 2572 CONECT 2572 2571 2573 2574 CONECT 2573 2572 2578 CONECT 2574 2572 2575 2576 CONECT 2575 2574 CONECT 2576 2574 2577 2578 CONECT 2577 2576 CONECT 2578 2573 2576 2579 CONECT 2579 2578 2580 2588 CONECT 2580 2579 2581 CONECT 2581 2580 2582 CONECT 2582 2581 2583 2588 CONECT 2583 2582 2584 2585 CONECT 2584 2583 CONECT 2585 2583 2586 CONECT 2586 2585 2587 CONECT 2587 2586 2588 CONECT 2588 2579 2582 2587 CONECT 2589 2611 CONECT 2590 2591 2595 2614 CONECT 2591 2590 2594 2596 CONECT 2592 2593 2595 2624 CONECT 2593 2592 2594 2605 CONECT 2594 2591 2593 2606 CONECT 2595 2590 2592 2619 CONECT 2596 2591 2611 CONECT 2597 2598 CONECT 2598 2597 2599 2600 2601 CONECT 2599 2598 CONECT 2600 2598 CONECT 2601 2598 2602 CONECT 2602 2601 2603 2604 2605 CONECT 2603 2602 CONECT 2604 2602 2633 CONECT 2605 2593 2602 CONECT 2606 2594 2607 CONECT 2607 2606 2608 2609 2610 CONECT 2608 2607 CONECT 2609 2607 CONECT 2610 2607 CONECT 2611 2589 2596 2612 2613 CONECT 2612 2611 CONECT 2613 2611 CONECT 2614 2590 2615 CONECT 2615 2614 2616 2617 2618 CONECT 2616 2615 CONECT 2617 2615 CONECT 2618 2615 CONECT 2619 2595 2620 CONECT 2620 2619 2621 2622 2623 CONECT 2621 2620 CONECT 2622 2620 CONECT 2623 2620 CONECT 2624 2592 2625 CONECT 2625 2624 2626 2627 2628 CONECT 2626 2625 CONECT 2627 2625 2633 CONECT 2628 2625 CONECT 2629 2237 2238 2252 2561 CONECT 2629 2563 2728 CONECT 2630 2146 2238 2559 2568 CONECT 2630 2739 CONECT 2631 197 211 243 2705 CONECT 2631 2819 2866 CONECT 2632 2671 2685 2736 2752 CONECT 2632 2862 2896 CONECT 2633 2604 2627 2724 2733 CONECT 2633 2816 2893 CONECT 2634 2635 2636 CONECT 2635 2634 CONECT 2636 2634 2637 CONECT 2637 2636 CONECT 2638 2639 2640 2641 CONECT 2639 2638 CONECT 2640 2638 CONECT 2641 2638 CONECT 2642 2643 2644 CONECT 2643 2642 CONECT 2644 2642 2645 CONECT 2645 2644 CONECT 2646 2647 2648 CONECT 2647 2646 CONECT 2648 2646 2649 CONECT 2649 2648 CONECT 2650 2651 2652 CONECT 2651 2650 CONECT 2652 2650 2653 CONECT 2653 2652 CONECT 2654 2655 2656 2657 CONECT 2655 2654 CONECT 2656 2654 CONECT 2657 2654 CONECT 2658 2659 2660 CONECT 2659 2658 CONECT 2660 2658 2661 CONECT 2661 2660 CONECT 2662 2663 2664 CONECT 2663 2662 CONECT 2664 2662 2665 CONECT 2665 2664 CONECT 2671 2632 CONECT 2685 2632 CONECT 2705 2631 CONECT 2724 2633 CONECT 2728 2629 CONECT 2733 2633 CONECT 2736 2632 CONECT 2739 2630 CONECT 2752 2632 CONECT 2816 2633 CONECT 2819 2631 CONECT 2862 2632 CONECT 2866 2631 CONECT 2893 2633 CONECT 2896 2632 MASTER 404 0 15 10 18 0 38 6 2913 1 135 26 END