HEADER TRANSFERASE 27-AUG-15 5DGI TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN DIPHOSPHOINOSITOL TITLE 2 PENTAKISPHOSPHATE KINASE 2 (PPIP5K2) IN COMPLEX WITH ADP AND 3,5- TITLE 3 (PCP)2-IP4 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: 511693; 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 5DGI 1 REMARK REVDAT 4 18-DEC-19 5DGI 1 REMARK REVDAT 3 20-SEP-17 5DGI 1 REMARK REVDAT 2 24-AUG-16 5DGI 1 JRNL REVDAT 1 10-AUG-16 5DGI 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. 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) : 29.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 32118 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) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2116 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) : 2000 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 148 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2550 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 106 REMARK 3 SOLVENT ATOMS : 352 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : 0.29000 REMARK 3 B33 (A**2) : -0.26000 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): 0.242 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.120 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.519 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2814 ; 0.006 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3808 ; 1.189 ; 2.004 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 337 ; 5.020 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 128 ;36.157 ;23.984 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 479 ;11.504 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ; 9.069 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 414 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2096 ; 0.004 ; 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): 1312 ; 1.916 ; 2.449 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1647 ; 2.706 ; 3.660 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1502 ; 2.524 ; 2.734 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): 4598 ; 5.068 ;22.034 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): 2814 ; 1.357 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 115 ;42.725 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2973 ;20.308 ; 5.000 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 5DGI 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_1000213048. 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 : 34299 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 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 (%) : 97.6 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09300 REMARK 200 FOR THE DATA SET : 20.0000 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 (%) : 85.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.43300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 (%): 53.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% (W/V) PEG 3350, 20 MM MGCL2, 0.1 M REMARK 280 HEPES, PH 7.0, 1 MM ATP 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,WHILE ATP IN THE CRYSTALS WAS HYDROLYZED TO ADP. THE REMARK 280 CRYSTALS WERE SOAKED UNDER THE ABOVE STABILIZING BUFFER FOR REMARK 280 THREE DAYS WITH 2 MM COMPOUND., 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 44.13400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.61800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.10250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.61800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.13400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.10250 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 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 653 O HOH A 750 2.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 163 49.54 -94.07 REMARK 500 ASN A 165 38.29 -96.72 REMARK 500 ASP A 268 -11.70 -140.70 REMARK 500 ASP A 321 129.84 -170.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 852 DISTANCE = 5.95 ANGSTROMS 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 97.1 REMARK 620 3 ILE A 73 O 119.6 96.0 REMARK 620 4 HOH A 598 O 87.0 174.6 78.8 REMARK 620 5 HOH A 653 O 141.9 99.2 92.6 79.5 REMARK 620 6 HOH A 750 O 89.7 96.3 146.3 87.3 54.5 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 93.3 REMARK 620 3 ADP A 401 O3B 176.2 87.6 REMARK 620 4 ADP A 401 O2A 89.7 95.7 86.5 REMARK 620 5 HOH A 549 O 87.4 174.9 92.1 89.4 REMARK 620 6 HOH A 742 O 90.3 89.4 93.4 174.8 85.5 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 321 OD1 REMARK 620 2 ASP A 321 OD2 59.1 REMARK 620 3 ASN A 323 OD1 87.5 90.5 REMARK 620 4 ADP A 401 O1B 92.4 90.0 179.4 REMARK 620 5 HOH A 515 O 97.5 156.6 87.1 92.3 REMARK 620 6 HOH A 705 O 158.7 100.6 86.3 94.0 102.5 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 ADP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5A2 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 ACT A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 ACT A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 413 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DGH RELATED DB: PDB DBREF 5DGI A 41 366 UNP O43314 VIP2_HUMAN 41 366 SEQADV 5DGI GLY A 37 UNP O43314 EXPRESSION TAG SEQADV 5DGI SER A 38 UNP O43314 EXPRESSION TAG SEQADV 5DGI PHE A 39 UNP O43314 EXPRESSION TAG SEQADV 5DGI THR A 40 UNP O43314 EXPRESSION TAG SEQRES 1 A 330 GLY SER PHE THR GLU ARG GLN ILE VAL VAL GLY ILE CYS SEQRES 2 A 330 SER MET ALA LYS LYS SER LYS SER LYS PRO MET LYS GLU SEQRES 3 A 330 ILE LEU GLU ARG ILE SER LEU PHE LYS TYR ILE THR VAL SEQRES 4 A 330 VAL VAL PHE GLU GLU GLU VAL ILE LEU ASN GLU PRO VAL SEQRES 5 A 330 GLU ASN TRP PRO LEU CYS ASP CYS LEU ILE SER PHE HIS SEQRES 6 A 330 SER LYS GLY PHE PRO LEU ASP LYS ALA VAL ALA TYR ALA SEQRES 7 A 330 LYS LEU ARG ASN PRO PHE VAL ILE ASN ASP LEU ASN MET SEQRES 8 A 330 GLN TYR LEU ILE GLN ASP ARG ARG GLU VAL TYR SER ILE SEQRES 9 A 330 LEU GLN ALA GLU GLY ILE LEU LEU PRO ARG TYR ALA ILE SEQRES 10 A 330 LEU ASN ARG ASP PRO ASN ASN PRO LYS GLU CYS ASN LEU SEQRES 11 A 330 ILE GLU GLY GLU ASP HIS VAL GLU VAL ASN GLY GLU VAL SEQRES 12 A 330 PHE GLN LYS PRO PHE VAL GLU LYS PRO VAL SER ALA GLU SEQRES 13 A 330 ASP HIS ASN VAL TYR ILE TYR TYR PRO THR SER ALA GLY SEQRES 14 A 330 GLY GLY SER GLN ARG LEU PHE ARG LYS ILE GLY SER ARG SEQRES 15 A 330 SER SER VAL TYR SER PRO GLU SER ASN VAL ARG LYS THR SEQRES 16 A 330 GLY SER TYR ILE TYR GLU GLU PHE MET PRO THR ASP GLY SEQRES 17 A 330 THR ASP VAL LYS VAL TYR THR VAL GLY PRO ASP TYR ALA SEQRES 18 A 330 HIS ALA GLU ALA ARG LYS SER PRO ALA LEU ASP GLY LYS SEQRES 19 A 330 VAL GLU ARG ASP SER GLU GLY LYS GLU VAL ARG TYR PRO SEQRES 20 A 330 VAL ILE LEU ASN ALA ARG GLU LYS LEU ILE ALA TRP LYS SEQRES 21 A 330 VAL CYS LEU ALA PHE LYS GLN THR VAL CYS GLY PHE ASP SEQRES 22 A 330 LEU LEU ARG ALA ASN GLY GLN SER TYR VAL CYS ASP VAL SEQRES 23 A 330 ASN GLY PHE SER PHE VAL LYS ASN SER MET LYS TYR TYR SEQRES 24 A 330 ASP ASP CYS ALA LYS ILE LEU GLY ASN ILE VAL MET ARG SEQRES 25 A 330 GLU LEU ALA PRO GLN PHE HIS ILE PRO TRP SER ILE PRO SEQRES 26 A 330 LEU GLU ALA GLU ASP HET ADP A 401 27 HET 5A2 A 402 53 HET MG A 403 1 HET MG A 404 1 HET MG A 405 1 HET ACT A 406 4 HET EDO A 407 4 HET ACT A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET EDO A 411 4 HET ACT A 412 4 HET EDO A 413 4 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM 5A2 3,5-DI-METHYLENEBISPHOSPHONATE INOSITOL HETNAM 2 5A2 TETRAKISPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN 5A2 {[(1R,3S,4R,5S,6R)-2,4,5,6-TETRAKIS(PHOSPHONOOXY) HETSYN 2 5A2 CYCLOHEXANE-1,3-DIYL]BIS[OXY(HYDROXYPHOSPHORYL) HETSYN 3 5A2 METHANEDIYL]}BIS(PHOSPHONIC ACID) HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 5A2 C8 H24 O28 P8 FORMUL 4 MG 3(MG 2+) FORMUL 7 ACT 3(C2 H3 O2 1-) FORMUL 8 EDO 5(C2 H6 O2) FORMUL 15 HOH *352(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 PHE A 301 1 15 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 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 VAL A 221 N ARG A 210 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 LEU A 310 N VAL A 247 SHEET 5 AA4 5 GLN A 316 GLY A 324 -1 O ASN A 323 N GLY A 307 LINK O SER A 68 MG MG A 405 1555 1555 2.20 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 2.15 LINK OD1 ASP A 321 MG MG A 403 1555 1555 2.21 LINK OD2 ASP A 321 MG MG A 403 1555 1555 2.18 LINK OD2 ASP A 321 MG MG A 404 1555 1555 2.17 LINK OD1 ASN A 323 MG MG A 403 1555 1555 2.17 LINK O1B ADP A 401 MG MG A 403 1555 1555 2.16 LINK O3B ADP A 401 MG MG A 404 1555 1555 2.15 LINK O2A ADP A 401 MG MG A 404 1555 1555 2.16 LINK MG MG A 403 O HOH A 515 1555 1555 2.16 LINK MG MG A 403 O HOH A 705 1555 1555 2.17 LINK MG MG A 404 O HOH A 549 1555 1555 2.18 LINK MG MG A 404 O HOH A 742 1555 1555 2.17 LINK MG MG A 405 O HOH A 598 1555 1555 2.19 LINK MG MG A 405 O HOH A 653 1555 1555 2.18 LINK MG MG A 405 O HOH A 750 1555 1555 2.18 CISPEP 1 LYS A 182 PRO A 183 0 3.96 SITE 1 AC1 23 ARG A 134 PRO A 149 VAL A 185 LYS A 187 SITE 2 AC1 23 HIS A 194 LEU A 211 GLU A 237 GLU A 238 SITE 3 AC1 23 PHE A 239 MET A 240 ASP A 246 SER A 264 SITE 4 AC1 23 PRO A 265 ASP A 309 LEU A 311 CYS A 320 SITE 5 AC1 23 ASP A 321 MG A 403 MG A 404 HOH A 519 SITE 6 AC1 23 HOH A 549 HOH A 694 HOH A 736 SITE 1 AC2 22 LYS A 53 LYS A 54 SER A 102 LYS A 103 SITE 2 AC2 22 ARG A 213 LYS A 214 TYR A 250 ARG A 262 SITE 3 AC2 22 ARG A 273 SER A 326 LYS A 329 HOH A 506 SITE 4 AC2 22 HOH A 512 HOH A 522 HOH A 557 HOH A 578 SITE 5 AC2 22 HOH A 589 HOH A 665 HOH A 703 HOH A 710 SITE 6 AC2 22 HOH A 743 HOH A 747 SITE 1 AC3 5 ASP A 321 ASN A 323 ADP A 401 HOH A 515 SITE 2 AC3 5 HOH A 705 SITE 1 AC4 5 ASP A 309 ASP A 321 ADP A 401 HOH A 549 SITE 2 AC4 5 HOH A 742 SITE 1 AC5 6 SER A 68 PHE A 70 ILE A 73 HOH A 598 SITE 2 AC5 6 HOH A 653 HOH A 750 SITE 1 AC6 6 VAL A 121 ASP A 124 LEU A 125 ASN A 126 SITE 2 AC6 6 HOH A 612 HOH A 658 SITE 1 AC7 7 ASN A 90 TRP A 91 PRO A 92 PRO A 283 SITE 2 AC7 7 ILE A 285 HOH A 554 HOH A 741 SITE 1 AC8 6 SER A 217 ARG A 218 LYS A 270 LYS A 291 SITE 2 AC8 6 LEU A 292 HOH A 542 SITE 1 AC9 8 LYS A 248 TYR A 250 GLY A 307 PHE A 308 SITE 2 AC9 8 ASP A 309 ASN A 323 SER A 326 HOH A 522 SITE 1 AD1 7 ARG A 312 ALA A 313 GLY A 315 GLN A 316 SITE 2 AD1 7 SER A 317 HOH A 518 HOH A 527 SITE 1 AD2 7 GLU A 89 ASN A 90 TYR A 256 HIS A 258 SITE 2 AD2 7 LYS A 333 TYR A 334 HOH A 737 SITE 1 AD3 2 PHE A 70 HOH A 656 SITE 1 AD4 6 PHE A 105 PRO A 106 LEU A 107 ASP A 108 SITE 2 AD4 6 HOH A 501 HOH A 607 CRYST1 88.268 110.205 41.236 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 0.011329 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009074 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024251 0.00000