HEADER TRANSFERASE 10-JUN-15 5BYA TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN DIPHOSPHOINOSITOL TITLE 2 PENTAKISPHOSPHATE KINASE 2 (PPIP5K2) IN COMPLEX WITH ADP AND 1,5- 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 FRAGMENT: UNP RESIDUES 42-359; 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: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ARCTIC EXPRESS (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST566 KEYWDS METHYLENEBISPHOSPHONATE, PHOSPHONOACETATE, NON-HYDROLYZABLE, KEYWDS 2 PYROPHOSPHATE MIMICS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,S.B.SHEARS REVDAT 3 27-SEP-23 5BYA 1 REMARK LINK REVDAT 2 26-AUG-15 5BYA 1 JRNL REVDAT 1 22-JUL-15 5BYA 0 JRNL AUTH A.M.RILEY,H.WANG,S.B.SHEARS,B.V.L POTTER JRNL TITL SYNTHETIC TOOLS FOR STUDYING THE CHEMICAL BIOLOGY OF INSP8. JRNL REF CHEM.COMMUN.(CAMB.) V. 51 12605 2015 JRNL REFN ESSN 1364-548X JRNL PMID 26153667 JRNL DOI 10.1039/C5CC05017K REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 30891 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 REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2017 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2208 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.1790 REMARK 3 BIN FREE R VALUE SET COUNT : 137 REMARK 3 BIN FREE R VALUE : 0.2680 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 : 112 REMARK 3 SOLVENT ATOMS : 445 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.60000 REMARK 3 B22 (A**2) : -0.30000 REMARK 3 B33 (A**2) : -0.29000 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): 0.308 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.622 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2762 ; 0.007 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3751 ; 1.327 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 329 ; 5.264 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 127 ;37.375 ;24.252 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 472 ;12.461 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;13.155 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 405 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2074 ; 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): 1302 ; 1.834 ; 1.874 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1630 ; 2.514 ; 2.795 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1460 ; 2.249 ; 2.134 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): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2762 ; 2.096 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 107 ;33.360 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3047 ;13.065 ; 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: U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5BYA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210707. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-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-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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32965 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11300 REMARK 200 FOR THE DATA SET : 15.7600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.66800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.420 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3T7A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 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 ANALOG., 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 44.28350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.72750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.72750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.28350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.20000 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 620 O HOH A 899 2.07 REMARK 500 O HOH A 559 O HOH A 899 2.18 REMARK 500 NZ LYS A 333 O HOH A 501 2.19 REMARK 500 O HOH A 708 O HOH A 880 2.19 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 ASN A 165 65.69 -109.91 REMARK 500 LEU A 267 -77.73 -66.24 REMARK 500 ASP A 321 129.55 -170.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 68 O REMARK 620 2 PHE A 70 O 93.2 REMARK 620 3 ILE A 73 O 117.2 91.2 REMARK 620 4 HOH A 590 O 149.2 104.7 87.7 REMARK 620 5 HOH A 804 O 83.9 169.9 81.6 82.2 REMARK 620 6 HOH A 816 O 80.6 93.6 161.3 73.6 95.5 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 93.4 REMARK 620 3 ADP A 401 O3B 173.7 87.1 REMARK 620 4 ADP A 401 O2A 88.3 91.1 85.4 REMARK 620 5 4WZ A 402 O51 95.8 86.5 90.6 175.4 REMARK 620 6 HOH A 568 O 86.7 179.1 92.8 88.0 94.4 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 58.0 REMARK 620 3 ASN A 323 OD1 86.7 89.8 REMARK 620 4 ADP A 401 O1B 93.6 88.9 178.2 REMARK 620 5 HOH A 596 O 154.9 97.9 85.9 93.0 REMARK 620 6 HOH A 599 O 102.9 160.6 85.3 96.4 100.4 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 4WZ A 402 O46 REMARK 620 2 4WZ A 402 O21 87.0 REMARK 620 3 4WZ A 402 O61 83.7 92.1 REMARK 620 4 HOH A 657 O 177.8 91.4 97.9 REMARK 620 5 HOH A 719 O 94.3 175.8 92.0 87.1 REMARK 620 6 HOH A 740 O 94.1 90.6 176.4 84.4 85.4 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 HOH A 519 O REMARK 620 2 HOH A 563 O 84.0 REMARK 620 3 HOH A 597 O 171.7 87.8 REMARK 620 4 HOH A 664 O 93.9 173.8 94.4 REMARK 620 5 HOH A 713 O 88.8 84.0 91.9 90.2 REMARK 620 6 HOH A 885 O 86.7 87.8 91.5 97.9 171.0 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 ADP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4WZ 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 EDO A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 416 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5BYB RELATED DB: PDB DBREF 5BYA A 41 366 UNP O43314 VIP2_HUMAN 41 366 SEQADV 5BYA GLY A 37 UNP O43314 EXPRESSION TAG SEQADV 5BYA SER A 38 UNP O43314 EXPRESSION TAG SEQADV 5BYA PHE A 39 UNP O43314 EXPRESSION TAG SEQADV 5BYA 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 4WZ A 402 44 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 ACT A 415 4 HET ACT A 416 4 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM 4WZ {[(1R,3S,4S,5R,6S)-2,4,5,6-TETRAKIS(PHOSPHONOOXY) HETNAM 2 4WZ CYCLOHEXANE-1,3-DIYL]BIS[OXY(HYDROXYPHOSPHORYL) HETNAM 3 4WZ METHANEDIYL]}BIS(PHOSPHONIC ACID) HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM ACT ACETATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 4WZ C8 H24 O28 P8 FORMUL 4 MG 5(MG 2+) FORMUL 9 EDO 5(C2 H6 O2) FORMUL 10 ACT 4(C2 H3 O2 1-) FORMUL 18 HOH *445(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 VAL A 46 O THR A 74 SHEET 3 AA1 4 CYS A 96 SER A 99 1 O ILE A 98 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 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 CYS A 306 N THR A 251 SHEET 5 AA4 5 GLN A 316 GLY A 324 -1 O TYR A 318 N LEU A 311 LINK O SER A 68 MG MG A 405 1555 1555 2.37 LINK O PHE A 70 MG MG A 405 1555 1555 2.29 LINK O ILE A 73 MG MG A 405 1555 1555 2.37 LINK OD2 ASP A 309 MG MG A 404 1555 1555 2.08 LINK OD1 ASP A 321 MG MG A 403 1555 1555 2.31 LINK OD2 ASP A 321 MG MG A 403 1555 1555 2.15 LINK OD2 ASP A 321 MG MG A 404 1555 1555 2.22 LINK OD1 ASN A 323 MG MG A 403 1555 1555 2.09 LINK O1B ADP A 401 MG MG A 403 1555 1555 2.00 LINK O3B ADP A 401 MG MG A 404 1555 1555 2.04 LINK O2A ADP A 401 MG MG A 404 1555 1555 2.08 LINK O51 4WZ A 402 MG MG A 404 1555 1555 2.17 LINK O46 4WZ A 402 MG MG A 406 1555 1555 2.39 LINK O21 4WZ A 402 MG MG A 406 1555 1555 2.02 LINK O61 4WZ A 402 MG MG A 406 1555 1555 1.92 LINK MG MG A 403 O HOH A 596 1555 1555 2.11 LINK MG MG A 403 O HOH A 599 1555 1555 2.02 LINK MG MG A 404 O HOH A 568 1555 1555 2.10 LINK MG MG A 405 O HOH A 590 1555 1555 2.26 LINK MG MG A 405 O HOH A 804 1555 1555 2.34 LINK MG MG A 405 O HOH A 816 1555 1555 2.44 LINK MG MG A 406 O HOH A 657 1555 1555 2.14 LINK MG MG A 406 O HOH A 719 1555 1555 2.08 LINK MG MG A 406 O HOH A 740 1555 1555 2.08 LINK MG MG A 407 O HOH A 519 1555 1555 2.18 LINK MG MG A 407 O HOH A 563 1555 1555 2.26 LINK MG MG A 407 O HOH A 597 1555 1555 2.05 LINK MG MG A 407 O HOH A 664 1555 1555 2.08 LINK MG MG A 407 O HOH A 713 1555 1555 2.17 LINK MG MG A 407 O HOH A 885 1555 1555 2.22 CISPEP 1 LYS A 182 PRO A 183 0 3.60 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 GLU A 237 GLU A 238 SITE 3 AC1 26 PHE A 239 MET A 240 ASP A 246 SER A 264 SITE 4 AC1 26 PRO A 265 ASP A 309 LEU A 311 CYS A 320 SITE 5 AC1 26 ASP A 321 4WZ A 402 MG A 403 MG A 404 SITE 6 AC1 26 HOH A 524 HOH A 568 HOH A 596 HOH A 599 SITE 7 AC1 26 HOH A 657 HOH A 720 SITE 1 AC2 35 LYS A 53 LYS A 54 ARG A 213 LYS A 214 SITE 2 AC2 35 LYS A 248 ARG A 262 ASP A 309 ASP A 321 SITE 3 AC2 35 ASN A 323 SER A 326 LYS A 329 ADP A 401 SITE 4 AC2 35 MG A 404 MG A 406 EDO A 410 HOH A 528 SITE 5 AC2 35 HOH A 543 HOH A 546 HOH A 554 HOH A 568 SITE 6 AC2 35 HOH A 569 HOH A 575 HOH A 596 HOH A 597 SITE 7 AC2 35 HOH A 613 HOH A 618 HOH A 620 HOH A 657 SITE 8 AC2 35 HOH A 669 HOH A 674 HOH A 719 HOH A 736 SITE 9 AC2 35 HOH A 740 HOH A 748 HOH A 776 SITE 1 AC3 5 ASP A 321 ASN A 323 ADP A 401 HOH A 596 SITE 2 AC3 5 HOH A 599 SITE 1 AC4 5 ASP A 309 ASP A 321 ADP A 401 4WZ A 402 SITE 2 AC4 5 HOH A 568 SITE 1 AC5 6 SER A 68 PHE A 70 ILE A 73 HOH A 590 SITE 2 AC5 6 HOH A 804 HOH A 816 SITE 1 AC6 4 4WZ A 402 HOH A 657 HOH A 719 HOH A 740 SITE 1 AC7 6 HOH A 519 HOH A 563 HOH A 597 HOH A 664 SITE 2 AC7 6 HOH A 713 HOH A 885 SITE 1 AC8 8 ASN A 90 TRP A 91 PRO A 92 PRO A 283 SITE 2 AC8 8 ILE A 285 HOH A 644 HOH A 678 HOH A 741 SITE 1 AC9 5 SER A 217 ARG A 218 LEU A 292 TRP A 295 SITE 2 AC9 5 HOH A 571 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 4WZ A 402 SITE 1 AD2 8 ARG A 312 ALA A 313 GLY A 315 GLN A 316 SITE 2 AD2 8 SER A 317 HOH A 509 HOH A 703 HOH A 762 SITE 1 AD3 6 ASN A 90 TYR A 256 HIS A 258 TYR A 334 SITE 2 AD3 6 HOH A 501 HOH A 770 SITE 1 AD4 7 PHE A 105 PRO A 106 LEU A 107 ASP A 108 SITE 2 AD4 7 HOH A 503 HOH A 647 HOH A 670 SITE 1 AD5 7 HIS A 101 GLN A 128 ILE A 131 GLN A 132 SITE 2 AD5 7 HOH A 519 HOH A 526 HOH A 688 SITE 1 AD6 6 VAL A 121 ASP A 124 LEU A 125 ASN A 126 SITE 2 AD6 6 HOH A 530 HOH A 679 CRYST1 88.567 110.400 41.455 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 0.011291 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009058 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024123 0.00000