HEADER TRANSFERASE 21-NOV-18 6N5C TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PPIP5K2 IN COMPLEX WITH TITLE 2 AMPPNP AND 5-PCF2AM-INSP5 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 KEYWDS INOSITOL, INOSITOL POLYPHOSPHATE, INOSITOL PYROPHOSPHATE, ANALOG, KEYWDS 2 PHOSPHONODIFLUOROACETAMIDE, DIPHOSPHOINOSITOL PENTAKISPHOSPHATE, KEYWDS 3 KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,S.B.SHEARS,A.RILEY,B.POTTER REVDAT 3 11-OCT-23 6N5C 1 LINK REVDAT 2 18-DEC-19 6N5C 1 REMARK REVDAT 1 21-AUG-19 6N5C 0 JRNL AUTH A.M.RILEY,H.WANG,S.B.SHEARS,B.V.L.POTTER JRNL TITL SYNTHESIS OF AN ALPHA-PHOSPHONO-ALPHA , JRNL TITL 2 ALPHA-DIFLUOROACETAMIDE ANALOGUE OF THE DIPHOSPHOINOSITOL JRNL TITL 3 PENTAKISPHOSPHATE 5-INSP7. JRNL REF MEDCHEMCOMM V. 10 1165 2019 JRNL REFN ESSN 2040-2511 JRNL PMID 31391889 JRNL DOI 10.1039/C9MD00163H REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 27828 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 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 : 1839 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1982 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 138 REMARK 3 BIN FREE R VALUE : 0.2620 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 : 296 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.18000 REMARK 3 B22 (A**2) : 0.23000 REMARK 3 B33 (A**2) : -0.41000 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): 0.151 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.140 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.092 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.224 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 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): 2704 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2473 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3656 ; 1.563 ; 1.674 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5746 ; 1.261 ; 1.582 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 316 ; 6.726 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;36.675 ;22.536 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 457 ;13.212 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;13.562 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 347 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2919 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 548 ; 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): 1270 ; 1.644 ; 2.844 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1266 ; 1.633 ; 2.837 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1582 ; 2.806 ; 4.250 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1583 ; 2.805 ; 4.253 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1434 ; 1.938 ; 3.168 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1435 ; 1.937 ; 3.168 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2075 ; 3.203 ; 4.660 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3024 ; 5.968 ;34.963 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3022 ; 5.969 ;34.938 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 43 A 604 REMARK 3 ORIGIN FOR THE GROUP (A): -0.2463 15.3518 3.6164 REMARK 3 T TENSOR REMARK 3 T11: 0.0129 T22: 0.0082 REMARK 3 T33: 0.0048 T12: 0.0091 REMARK 3 T13: 0.0023 T23: 0.0044 REMARK 3 L TENSOR REMARK 3 L11: 0.2469 L22: 0.4513 REMARK 3 L33: 0.4454 L12: -0.2084 REMARK 3 L13: 0.0174 L23: -0.2967 REMARK 3 S TENSOR REMARK 3 S11: 0.0179 S12: 0.0169 S13: 0.0033 REMARK 3 S21: -0.0057 S22: 0.0134 S23: 0.0329 REMARK 3 S31: 0.0348 S32: 0.0003 S33: -0.0313 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6N5C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000238187. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-15 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 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29821 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 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 : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.3800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.630 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 3T9D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 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 2MM 5PCF2- REMARK 280 AM-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 44.30200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.71450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.51600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.71450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.30200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.51600 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 ASN A 160 59.43 -115.74 REMARK 500 GLU A 163 171.46 170.90 REMARK 500 LYS A 214 129.19 -36.89 REMARK 500 LEU A 267 -140.82 -65.40 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 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 68 O REMARK 620 2 PHE A 70 O 94.6 REMARK 620 3 ILE A 73 O 123.4 93.4 REMARK 620 4 HOH A 543 O 143.5 103.6 87.2 REMARK 620 5 HOH A 699 O 78.2 93.8 156.6 69.4 REMARK 620 6 HOH A 740 O 88.8 176.5 84.0 74.0 87.7 REMARK 620 N 1 2 3 4 5 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 309 OD2 REMARK 620 2 ASP A 321 OD2 95.1 REMARK 620 3 ANP A 401 O1G 107.0 87.3 REMARK 620 4 ANP A 401 O2A 110.8 93.2 142.0 REMARK 620 5 HOH A 565 O 81.4 176.1 92.1 89.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 321 OD1 REMARK 620 2 ASP A 321 OD2 61.9 REMARK 620 3 ANP A 401 O3G 154.9 93.2 REMARK 620 4 ANP A 401 O1B 90.6 83.2 89.8 REMARK 620 5 HOH A 600 O 101.4 163.3 103.4 97.4 REMARK 620 N 1 2 3 4 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 HOH A 524 O REMARK 620 2 HOH A 559 O 163.0 REMARK 620 3 HOH A 562 O 85.5 90.5 REMARK 620 4 HOH A 690 O 108.4 87.9 87.2 REMARK 620 5 HOH A 747 O 112.1 73.2 162.4 85.8 REMARK 620 6 HOH A 753 O 90.1 73.2 87.8 160.4 93.5 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 MG 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 KDJ A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT 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 DBREF 6N5C A 41 366 UNP O43314 VIP2_HUMAN 41 366 SEQADV 6N5C GLY A 37 UNP O43314 EXPRESSION TAG SEQADV 6N5C SER A 38 UNP O43314 EXPRESSION TAG SEQADV 6N5C PHE A 39 UNP O43314 EXPRESSION TAG SEQADV 6N5C 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 MG A 402 1 HET MG A 403 1 HET MG A 404 1 HET MG A 405 1 HET KDJ A 406 41 HET ACT A 407 4 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 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM KDJ (1,1-DIFLUORO-2-OXO-2-{[(1S,2R,3S,4S,5R,6S)-2,3,4,5,6- HETNAM 2 KDJ PENTAKIS(PHOSPHONOOXY)CYCLOHEXYL]AMINO}ETHYL) HETNAM 3 KDJ PHOSPHONIC ACID HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 MG 4(MG 2+) FORMUL 7 KDJ C8 H19 F2 N O24 P6 FORMUL 8 ACT 3(C2 H3 O2 1-) FORMUL 9 EDO 5(C2 H6 O2) FORMUL 16 HOH *296(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 HIS A 355 1 25 SHEET 1 AA1 4 ILE A 73 VAL A 77 0 SHEET 2 AA1 4 ILE A 44 CYS A 49 1 N VAL A 46 O THR A 74 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 PHE A 180 N VAL A 173 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 404 1555 1555 2.26 LINK O PHE A 70 MG MG A 404 1555 1555 2.21 LINK O ILE A 73 MG MG A 404 1555 1555 2.25 LINK OD2 ASP A 309 MG MG A 403 1555 1555 1.99 LINK OD1 ASP A 321 MG MG A 402 1555 1555 2.22 LINK OD2 ASP A 321 MG MG A 402 1555 1555 2.09 LINK OD2 ASP A 321 MG MG A 403 1555 1555 2.08 LINK O3G ANP A 401 MG MG A 402 1555 1555 2.01 LINK O1B ANP A 401 MG MG A 402 1555 1555 2.10 LINK O1G ANP A 401 MG MG A 403 1555 1555 1.92 LINK O2A ANP A 401 MG MG A 403 1555 1555 2.00 LINK MG MG A 402 O HOH A 600 1555 1555 2.05 LINK MG MG A 403 O HOH A 565 1555 1555 2.10 LINK MG MG A 404 O HOH A 543 1555 1555 2.31 LINK MG MG A 404 O HOH A 699 1555 1555 2.47 LINK MG MG A 404 O HOH A 740 1555 1555 2.60 LINK MG MG A 405 O HOH A 524 1555 1555 1.84 LINK MG MG A 405 O HOH A 559 1555 1555 2.34 LINK MG MG A 405 O HOH A 562 1555 1555 2.43 LINK MG MG A 405 O HOH A 690 1555 1555 2.07 LINK MG MG A 405 O HOH A 747 1555 1555 2.22 LINK MG MG A 405 O HOH A 753 1555 1555 2.11 CISPEP 1 LYS A 182 PRO A 183 0 3.38 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 402 MG A 403 SITE 6 AC1 26 KDJ A 406 HOH A 523 HOH A 565 HOH A 569 SITE 7 AC1 26 HOH A 572 HOH A 704 SITE 1 AC2 4 ASP A 321 ASN A 323 ANP A 401 HOH A 600 SITE 1 AC3 4 ASP A 309 ASP A 321 ANP A 401 HOH A 565 SITE 1 AC4 6 SER A 68 PHE A 70 ILE A 73 HOH A 543 SITE 2 AC4 6 HOH A 699 HOH A 740 SITE 1 AC5 6 HOH A 524 HOH A 559 HOH A 562 HOH A 690 SITE 2 AC5 6 HOH A 747 HOH A 753 SITE 1 AC6 24 LYS A 53 LYS A 54 ARG A 213 LYS A 214 SITE 2 AC6 24 LYS A 248 ARG A 262 ARG A 273 SER A 326 SITE 3 AC6 24 LYS A 329 ANP A 401 EDO A 410 HOH A 510 SITE 4 AC6 24 HOH A 515 HOH A 523 HOH A 524 HOH A 525 SITE 5 AC6 24 HOH A 553 HOH A 562 HOH A 575 HOH A 601 SITE 6 AC6 24 HOH A 605 HOH A 651 HOH A 657 HOH A 668 SITE 1 AC7 6 VAL A 121 ASP A 124 LEU A 125 ASN A 126 SITE 2 AC7 6 HOH A 521 HOH A 624 SITE 1 AC8 7 ASN A 90 TRP A 91 PRO A 92 ILE A 285 SITE 2 AC8 7 HOH A 638 HOH A 667 HOH A 703 SITE 1 AC9 4 SER A 217 ARG A 218 LEU A 292 HOH A 555 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 KDJ A 406 SITE 1 AD2 6 ARG A 312 ALA A 313 GLY A 315 GLN A 316 SITE 2 AD2 6 SER A 317 HOH A 514 SITE 1 AD3 4 ASN A 90 TYR A 256 HIS A 258 HOH A 584 SITE 1 AD4 2 PHE A 70 HOH A 673 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 574 CRYST1 88.604 111.032 41.429 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 0.011286 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009006 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024138 0.00000