HEADER TRANSFERASE 10-JUN-15 5BYB 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 (PA)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 41-366; COMPND 6 SYNONYM: DIPHOSPHOINOSITOL PENTAKISPHOSPHATE KINASE 2,HISTIDINE ACID COMPND 7 PHOSPHATASE DOMAIN-CONTAINING PROTEIN 1,INSP6 AND PP-IP5 KINASE 2, COMPND 8 VIP1 HOMOLOG 2,HSVIP2; COMPND 9 EC: 2.7.4.21,2.7.4.24; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PPIP5K2, HISPPD1, KIAA0433, VIP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 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 4 27-SEP-23 5BYB 1 LINK REVDAT 3 22-NOV-17 5BYB 1 REMARK REVDAT 2 05-AUG-15 5BYB 1 JRNL REVDAT 1 22-JUL-15 5BYB 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. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 17585 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1143 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1180 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.3350 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 : 100 REMARK 3 SOLVENT ATOMS : 206 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.00000 REMARK 3 B22 (A**2) : -0.32000 REMARK 3 B33 (A**2) : -0.68000 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): 0.309 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.235 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.154 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.292 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.885 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2750 ; 0.011 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3725 ; 1.738 ; 2.011 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 318 ; 5.752 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;38.103 ;24.228 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 459 ;14.636 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;12.632 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 409 ; 0.133 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2025 ; 0.006 ; 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): 1272 ; 1.761 ; 2.126 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1585 ; 3.129 ; 3.172 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1478 ; 1.783 ; 2.239 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): 4311 ; 6.811 ;17.767 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 5BYB 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_1000210713. 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000, XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18773 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11400 REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.43800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 (%): 56.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 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 44.40350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.71150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.20550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.71150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.40350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.20550 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 108 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 321 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES 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 LYS A 162 23.41 -142.48 REMARK 500 GLU A 163 41.12 -88.71 REMARK 500 ASN A 165 56.00 -97.52 REMARK 500 LYS A 214 125.33 -36.10 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 93.8 REMARK 620 3 ILE A 73 O 130.0 94.5 REMARK 620 4 HOH A 664 O 92.2 174.0 81.9 REMARK 620 5 HOH A 684 O 79.7 82.6 150.3 98.0 REMARK 620 N 1 2 3 4 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 93.5 REMARK 620 3 ADP A 401 O3B 156.9 85.0 REMARK 620 4 ADP A 401 O2A 84.5 81.7 72.5 REMARK 620 5 HOH A 525 O 84.4 161.1 89.6 79.4 REMARK 620 6 HOH A 645 O 117.8 88.2 85.2 156.2 109.5 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 58.3 REMARK 620 3 ASN A 323 OD1 75.9 91.0 REMARK 620 4 ADP A 401 O1B 91.1 84.5 166.7 REMARK 620 5 HOH A 583 O 93.2 151.3 84.5 93.4 REMARK 620 N 1 2 3 4 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 4WY 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 ACT 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 EDO A 412 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5BYA RELATED DB: PDB DBREF 5BYB A 41 366 UNP O43314 VIP2_HUMAN 41 366 SEQADV 5BYB GLY A 37 UNP O43314 EXPRESSION TAG SEQADV 5BYB SER A 38 UNP O43314 EXPRESSION TAG SEQADV 5BYB PHE A 39 UNP O43314 EXPRESSION TAG SEQADV 5BYB 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 4WY A 402 84 HET MG A 403 1 HET MG A 404 1 HET MG A 405 1 HET ACT A 406 4 HET ACT A 407 4 HET ACT A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET EDO A 411 4 HET EDO A 412 4 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM 4WY {[(1R,3S,4S,5R,6S)-2,4,5,6-TETRAKIS(PHOSPHONOOXY) HETNAM 2 4WY CYCLOHEXANE-1,3-DIYL]BIS[OXY(2-OXOETHANE-2,1-DIYL) HETNAM 3 4WY ]}BIS(PHOSPHONIC ACID) HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 4WY C10 H22 O26 P6 FORMUL 4 MG 3(MG 2+) FORMUL 7 ACT 3(C2 H3 O2 1-) FORMUL 10 EDO 4(C2 H6 O2) FORMUL 14 HOH *206(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 ILE A 44 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 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 2.19 LINK O PHE A 70 MG MG A 405 1555 1555 2.20 LINK O ILE A 73 MG MG A 405 1555 1555 2.21 LINK OD2 ASP A 309 MG MG A 404 1555 1555 2.15 LINK OD1 ASP A 321 MG MG A 403 1555 1555 2.22 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 2.15 LINK O1B ADP A 401 MG MG A 403 1555 1555 2.14 LINK O3B ADP A 401 MG MG A 404 1555 1555 2.13 LINK O2A ADP A 401 MG MG A 404 1555 1555 2.19 LINK MG MG A 403 O HOH A 583 1555 1555 2.00 LINK MG MG A 404 O HOH A 525 1555 1555 2.12 LINK MG MG A 404 O HOH A 645 1555 1555 2.20 LINK MG MG A 405 O HOH A 664 1555 1555 2.42 LINK MG MG A 405 O HOH A 684 1555 1555 2.66 CISPEP 1 LYS A 182 PRO A 183 0 -0.19 SITE 1 AC1 24 ARG A 134 PRO A 149 VAL A 185 LYS A 187 SITE 2 AC1 24 HIS A 194 LEU A 211 GLU A 237 GLU A 238 SITE 3 AC1 24 PHE A 239 MET A 240 ASP A 246 SER A 264 SITE 4 AC1 24 PRO A 265 ASP A 309 LEU A 311 CYS A 320 SITE 5 AC1 24 ASP A 321 MG A 403 MG A 404 HOH A 503 SITE 6 AC1 24 HOH A 525 HOH A 583 HOH A 632 HOH A 645 SITE 1 AC2 19 LYS A 53 LYS A 54 SER A 102 LYS A 103 SITE 2 AC2 19 GLU A 192 HIS A 194 ARG A 213 LYS A 214 SITE 3 AC2 19 LYS A 248 TYR A 250 ARG A 262 SER A 326 SITE 4 AC2 19 LYS A 329 HOH A 522 HOH A 535 HOH A 577 SITE 5 AC2 19 HOH A 580 HOH A 640 HOH A 644 SITE 1 AC3 4 ASP A 321 ASN A 323 ADP A 401 HOH A 583 SITE 1 AC4 5 ASP A 309 ASP A 321 ADP A 401 HOH A 525 SITE 2 AC4 5 HOH A 645 SITE 1 AC5 5 SER A 68 PHE A 70 ILE A 73 HOH A 664 SITE 2 AC5 5 HOH A 684 SITE 1 AC6 5 ASP A 124 LEU A 125 ASN A 126 HOH A 566 SITE 2 AC6 5 HOH A 655 SITE 1 AC7 2 PHE A 70 HOH A 668 SITE 1 AC8 5 SER A 217 ARG A 218 LYS A 291 TRP A 295 SITE 2 AC8 5 HOH A 532 SITE 1 AC9 6 ASN A 287 ARG A 289 ARG A 312 GLY A 315 SITE 2 AC9 6 GLN A 316 HOH A 602 SITE 1 AD1 4 ASN A 90 TYR A 256 HIS A 258 LYS A 333 SITE 1 AD2 7 ASN A 90 TRP A 91 PRO A 92 PRO A 283 SITE 2 AD2 7 ILE A 285 HOH A 575 HOH A 613 SITE 1 AD3 7 PHE A 105 PRO A 106 LEU A 107 ASP A 108 SITE 2 AD3 7 HOH A 501 HOH A 507 HOH A 621 CRYST1 88.807 110.411 41.423 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 0.011260 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009057 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024141 0.00000