PDB Short entry for 2VPF HEADER GROWTH FACTOR 29-JUL-97 2VPF TITLE VASCULAR ENDOTHELIAL GROWTH FACTOR REFINED TO 1.93 ANGSTROMS TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN, RESIDUES 8 - 109; COMPND 5 SYNONYM: VEGF, VASCULAR PERMEABILITY FACTOR, VPF; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM KEYWDS GROWTH FACTOR, CYSTINE KNOT, ANGIOGENESIS, VASCULOGENESIS EXPDTA X-RAY DIFFRACTION AUTHOR Y.A.MULLER,A.M.DE VOS REVDAT 4 09-AUG-23 2VPF 1 REMARK REVDAT 3 24-FEB-09 2VPF 1 VERSN REVDAT 2 01-APR-03 2VPF 1 JRNL REVDAT 1 29-JUL-98 2VPF 0 JRNL AUTH Y.A.MULLER,H.W.CHRISTINGER,B.A.KEYT,A.M.DE VOS JRNL TITL THE CRYSTAL STRUCTURE OF VASCULAR ENDOTHELIAL GROWTH FACTOR JRNL TITL 2 (VEGF) REFINED TO 1.93 A RESOLUTION: MULTIPLE COPY JRNL TITL 3 FLEXIBILITY AND RECEPTOR BINDING. JRNL REF STRUCTURE V. 5 1325 1997 JRNL REFN ISSN 0969-2126 JRNL PMID 9351807 JRNL DOI 10.1016/S0969-2126(97)00284-0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.A.MULLER,B.LI,H.W.CHRISTINGER,J.A.WELLS,B.C.CUNNINGHAM, REMARK 1 AUTH 2 A.M.DE VOS REMARK 1 TITL VASCULAR ENDOTHELIAL GROWTH FACTOR: CRYSTAL STRUCTURE AND REMARK 1 TITL 2 FUNCTIONAL MAPPING OF THE KINASE DOMAIN RECEPTOR BINDING REMARK 1 TITL 3 SITE REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 94 7192 1997 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.W.CHRISTINGER,Y.A.MULLER,L.T.BERLEAU,B.A.KEYT, REMARK 1 AUTH 2 B.C.CUNNINGHAM,N.FERRARA,A.M.DE VOS REMARK 1 TITL CRYSTALLIZATION OF THE RECEPTOR BINDING DOMAIN OF VASCULAR REMARK 1 TITL 2 ENDOTHELIAL GROWTH FACTOR REMARK 1 REF PROTEINS V. 26 353 1996 REMARK 1 REFN ISSN 0887-3585 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 68901 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RESOLUTION SHELLS REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7074 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6142 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.56000 REMARK 3 B22 (A**2) : 3.09000 REMARK 3 B33 (A**2) : 5.47000 REMARK 3 B12 (A**2) : 0.76000 REMARK 3 B13 (A**2) : 1.22000 REMARK 3 B23 (A**2) : 1.64000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.011 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.030 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.032 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.113 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.179 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.243 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.189 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.100 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 18.200; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 29.900; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.010 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.778 ; 4.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.468 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.892 ; 4.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AN EXPLICIT BULK SOLVENT MASK WAS REMARK 3 CALCULATED WITH PROGRAM X-PLOR AND INTRODUCED INTO REFMAC USING REMARK 3 PARTIAL STRUCTURE FACTORS (F-PART) REMARK 4 REMARK 4 2VPF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178740. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAR-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : PRINCETON 2K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72050 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.4000 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) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.12700 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1VPF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP, CRYSTALLIZED FROM 14 % REMARK 280 PEG3350, 10% ISOPROPANOL, 0.2 M AMMONIUM ACETATE PH 5.6, VAPOR REMARK 280 DIFFUSION - HANGING DROP, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H 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 8 REMARK 465 GLN A 9 REMARK 465 ASN A 10 REMARK 465 HIS A 11 REMARK 465 HIS A 12 REMARK 465 GLY B 8 REMARK 465 GLN B 9 REMARK 465 ASN B 10 REMARK 465 HIS B 11 REMARK 465 HIS B 12 REMARK 465 ASP B 109 REMARK 465 GLY C 8 REMARK 465 GLN C 9 REMARK 465 ASN C 10 REMARK 465 HIS C 11 REMARK 465 HIS C 12 REMARK 465 GLU C 13 REMARK 465 LYS C 107 REMARK 465 LYS C 108 REMARK 465 ASP C 109 REMARK 465 GLY D 8 REMARK 465 GLN D 9 REMARK 465 ASN D 10 REMARK 465 HIS D 11 REMARK 465 HIS D 12 REMARK 465 LYS D 108 REMARK 465 ASP D 109 REMARK 465 GLY E 8 REMARK 465 GLN E 9 REMARK 465 ASN E 10 REMARK 465 HIS E 11 REMARK 465 HIS E 12 REMARK 465 ASP E 109 REMARK 465 GLY F 8 REMARK 465 GLN F 9 REMARK 465 ASN F 10 REMARK 465 HIS F 11 REMARK 465 HIS F 12 REMARK 465 ASP F 109 REMARK 465 GLY G 8 REMARK 465 GLN G 9 REMARK 465 ASN G 10 REMARK 465 HIS G 11 REMARK 465 HIS G 12 REMARK 465 LYS G 108 REMARK 465 ASP G 109 REMARK 465 GLY H 8 REMARK 465 GLN H 9 REMARK 465 ASN H 10 REMARK 465 HIS H 11 REMARK 465 HIS H 12 REMARK 465 GLU H 13 REMARK 465 LYS H 108 REMARK 465 ASP H 109 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 13 CG CD OE1 OE2 REMARK 470 LYS A 108 CG CD CE NZ REMARK 470 ASP A 109 CG OD1 OD2 REMARK 470 GLU B 13 CG CD OE1 OE2 REMARK 470 GLU D 13 CG CD OE1 OE2 REMARK 470 GLU E 13 CG CD OE1 OE2 REMARK 470 GLU F 13 CG CD OE1 OE2 REMARK 470 LYS F 108 CG CD CE NZ REMARK 470 GLU G 13 CG CD OE1 OE2 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 ARG A 23 CD - NE - CZ ANGL. DEV. = 12.3 DEGREES REMARK 500 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG A 23 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 GLU A 72 OE1 - CD - OE2 ANGL. DEV. = -8.2 DEGREES REMARK 500 ARG A 105 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG B 23 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG B 56 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 VAL C 20 CB - CA - C ANGL. DEV. = -12.7 DEGREES REMARK 500 ARG C 56 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG C 56 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG C 82 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 VAL D 20 CB - CA - C ANGL. DEV. = -12.0 DEGREES REMARK 500 ARG D 23 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG E 23 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG F 23 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 MET F 81 CA - CB - CG ANGL. DEV. = 17.4 DEGREES REMARK 500 GLN F 87 CA - C - N ANGL. DEV. = 12.1 DEGREES REMARK 500 CYS G 51 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP H 34 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP H 34 CB - CG - OD2 ANGL. DEV. = -6.0 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 CYS A 26 110.67 -16.96 REMARK 500 GLU A 42 50.27 -96.09 REMARK 500 LYS A 108 -157.82 -123.68 REMARK 500 CYS B 26 114.00 -16.31 REMARK 500 GLU B 42 43.58 -87.81 REMARK 500 ASP B 63 113.76 178.44 REMARK 500 CYS C 26 119.55 -22.18 REMARK 500 GLU C 42 56.28 -91.89 REMARK 500 HIS C 86 -3.25 75.96 REMARK 500 CYS D 26 119.44 -13.17 REMARK 500 GLN D 87 31.56 -152.55 REMARK 500 CYS E 26 116.24 -19.20 REMARK 500 CYS F 26 114.56 -24.70 REMARK 500 GLU F 42 58.02 -92.15 REMARK 500 ASP F 63 117.46 -179.63 REMARK 500 HIS F 86 10.42 57.36 REMARK 500 CYS G 26 117.60 -28.69 REMARK 500 ASP G 63 115.82 -167.00 REMARK 500 CYS H 26 114.92 -29.28 REMARK 500 GLU H 42 55.43 -114.28 REMARK 500 ASP H 63 128.93 177.02 REMARK 500 HIS H 86 -3.08 67.08 REMARK 500 REMARK 500 REMARK: NULL DBREF 2VPF A 8 109 UNP P15692 VEGFA_HUMAN 34 135 DBREF 2VPF B 8 109 UNP P15692 VEGFA_HUMAN 34 135 DBREF 2VPF C 8 109 UNP P15692 VEGFA_HUMAN 34 135 DBREF 2VPF D 8 109 UNP P15692 VEGFA_HUMAN 34 135 DBREF 2VPF E 8 109 UNP P15692 VEGFA_HUMAN 34 135 DBREF 2VPF F 8 109 UNP P15692 VEGFA_HUMAN 34 135 DBREF 2VPF G 8 109 UNP P15692 VEGFA_HUMAN 34 135 DBREF 2VPF H 8 109 UNP P15692 VEGFA_HUMAN 34 135 SEQRES 1 A 102 GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP VAL SEQRES 2 A 102 TYR GLN ARG SER TYR CYS HIS PRO ILE GLU THR LEU VAL SEQRES 3 A 102 ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE SEQRES 4 A 102 PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY GLY SEQRES 5 A 102 CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR GLU SEQRES 6 A 102 GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS PRO SEQRES 7 A 102 HIS GLN GLY GLN HIS ILE GLY GLU MET SER PHE LEU GLN SEQRES 8 A 102 HIS ASN LYS CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 B 102 GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP VAL SEQRES 2 B 102 TYR GLN ARG SER TYR CYS HIS PRO ILE GLU THR LEU VAL SEQRES 3 B 102 ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE SEQRES 4 B 102 PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY GLY SEQRES 5 B 102 CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR GLU SEQRES 6 B 102 GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS PRO SEQRES 7 B 102 HIS GLN GLY GLN HIS ILE GLY GLU MET SER PHE LEU GLN SEQRES 8 B 102 HIS ASN LYS CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 C 102 GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP VAL SEQRES 2 C 102 TYR GLN ARG SER TYR CYS HIS PRO ILE GLU THR LEU VAL SEQRES 3 C 102 ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE SEQRES 4 C 102 PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY GLY SEQRES 5 C 102 CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR GLU SEQRES 6 C 102 GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS PRO SEQRES 7 C 102 HIS GLN GLY GLN HIS ILE GLY GLU MET SER PHE LEU GLN SEQRES 8 C 102 HIS ASN LYS CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 D 102 GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP VAL SEQRES 2 D 102 TYR GLN ARG SER TYR CYS HIS PRO ILE GLU THR LEU VAL SEQRES 3 D 102 ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE SEQRES 4 D 102 PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY GLY SEQRES 5 D 102 CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR GLU SEQRES 6 D 102 GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS PRO SEQRES 7 D 102 HIS GLN GLY GLN HIS ILE GLY GLU MET SER PHE LEU GLN SEQRES 8 D 102 HIS ASN LYS CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 E 102 GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP VAL SEQRES 2 E 102 TYR GLN ARG SER TYR CYS HIS PRO ILE GLU THR LEU VAL SEQRES 3 E 102 ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE SEQRES 4 E 102 PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY GLY SEQRES 5 E 102 CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR GLU SEQRES 6 E 102 GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS PRO SEQRES 7 E 102 HIS GLN GLY GLN HIS ILE GLY GLU MET SER PHE LEU GLN SEQRES 8 E 102 HIS ASN LYS CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 F 102 GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP VAL SEQRES 2 F 102 TYR GLN ARG SER TYR CYS HIS PRO ILE GLU THR LEU VAL SEQRES 3 F 102 ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE SEQRES 4 F 102 PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY GLY SEQRES 5 F 102 CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR GLU SEQRES 6 F 102 GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS PRO SEQRES 7 F 102 HIS GLN GLY GLN HIS ILE GLY GLU MET SER PHE LEU GLN SEQRES 8 F 102 HIS ASN LYS CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 G 102 GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP VAL SEQRES 2 G 102 TYR GLN ARG SER TYR CYS HIS PRO ILE GLU THR LEU VAL SEQRES 3 G 102 ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE SEQRES 4 G 102 PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY GLY SEQRES 5 G 102 CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR GLU SEQRES 6 G 102 GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS PRO SEQRES 7 G 102 HIS GLN GLY GLN HIS ILE GLY GLU MET SER PHE LEU GLN SEQRES 8 G 102 HIS ASN LYS CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 H 102 GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP VAL SEQRES 2 H 102 TYR GLN ARG SER TYR CYS HIS PRO ILE GLU THR LEU VAL SEQRES 3 H 102 ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE SEQRES 4 H 102 PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY GLY SEQRES 5 H 102 CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR GLU SEQRES 6 H 102 GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS PRO SEQRES 7 H 102 HIS GLN GLY GLN HIS ILE GLY GLU MET SER PHE LEU GLN SEQRES 8 H 102 HIS ASN LYS CYS GLU CYS ARG PRO LYS LYS ASP FORMUL 9 HOH *640(H2 O) HELIX 1 1 PHE A 17 SER A 24 1 8 HELIX 2 2 ILE A 35 GLU A 38 1 4 HELIX 3 3 PHE B 17 SER B 24 1 8 HELIX 4 4 ILE B 35 GLU B 38 1 4 HELIX 5 5 PHE C 17 ARG C 23 1 7 HELIX 6 6 ILE C 35 GLU C 38 1 4 HELIX 7 7 PHE D 17 ARG D 23 1 7 HELIX 8 8 ILE D 35 GLU D 38 1 4 HELIX 9 9 PHE E 17 SER E 24 1 8 HELIX 10 10 ILE E 35 GLU E 38 1 4 HELIX 11 11 PHE F 17 SER F 24 1 8 HELIX 12 12 ILE F 35 GLU F 38 1 4 HELIX 13 13 PHE G 17 SER G 24 1 8 HELIX 14 14 ILE G 35 GLU G 38 1 4 HELIX 15 15 PHE H 17 SER H 24 1 8 HELIX 16 16 ILE H 35 GLU H 38 1 4 SHEET 1 A 2 HIS A 27 ASP A 34 0 SHEET 2 A 2 CYS A 51 GLY A 58 -1 N GLY A 58 O HIS A 27 SHEET 1 B 3 ILE A 46 LYS A 48 0 SHEET 2 B 3 GLU A 73 ILE A 83 -1 N ILE A 83 O ILE A 46 SHEET 3 B 3 GLN A 89 HIS A 99 -1 N GLN A 98 O SER A 74 SHEET 1 C 2 LEU A 66 GLU A 72 0 SHEET 2 C 2 LYS A 101 PRO A 106 -1 N ARG A 105 O GLU A 67 SHEET 1 D 2 HIS B 27 ASP B 34 0 SHEET 2 D 2 CYS B 51 GLY B 58 -1 N GLY B 58 O HIS B 27 SHEET 1 E 3 ILE B 46 LYS B 48 0 SHEET 2 E 3 GLU B 73 ILE B 83 -1 N ILE B 83 O ILE B 46 SHEET 3 E 3 GLN B 89 HIS B 99 -1 N GLN B 98 O SER B 74 SHEET 1 F 2 LEU B 66 GLU B 72 0 SHEET 2 F 2 LYS B 101 PRO B 106 -1 N ARG B 105 O GLU B 67 SHEET 1 G 2 HIS C 27 ASP C 34 0 SHEET 2 G 2 CYS C 51 GLY C 58 -1 N GLY C 58 O HIS C 27 SHEET 1 H 3 ILE C 46 LYS C 48 0 SHEET 2 H 3 GLU C 73 LYS C 84 -1 N ILE C 83 O ILE C 46 SHEET 3 H 3 GLY C 88 HIS C 99 -1 N GLN C 98 O SER C 74 SHEET 1 I 2 GLU C 67 GLU C 72 0 SHEET 2 I 2 LYS C 101 ARG C 105 -1 N ARG C 105 O GLU C 67 SHEET 1 J 2 HIS D 27 ASP D 34 0 SHEET 2 J 2 CYS D 51 GLY D 58 -1 N GLY D 58 O HIS D 27 SHEET 1 K 3 TYR D 45 LYS D 48 0 SHEET 2 K 3 GLU D 73 LYS D 84 -1 N ILE D 83 O ILE D 46 SHEET 3 K 3 GLN D 89 HIS D 99 -1 N GLN D 98 O SER D 74 SHEET 1 L 2 LEU D 66 GLU D 72 0 SHEET 2 L 2 LYS D 101 PRO D 106 -1 N ARG D 105 O GLU D 67 SHEET 1 M 2 HIS E 27 ASP E 34 0 SHEET 2 M 2 CYS E 51 GLY E 58 -1 N GLY E 58 O HIS E 27 SHEET 1 N 3 ILE E 46 LYS E 48 0 SHEET 2 N 3 GLU E 73 LYS E 84 -1 N ILE E 83 O ILE E 46 SHEET 3 N 3 GLY E 88 HIS E 99 -1 N GLN E 98 O SER E 74 SHEET 1 O 2 LEU E 66 GLU E 72 0 SHEET 2 O 2 LYS E 101 PRO E 106 -1 N ARG E 105 O GLU E 67 SHEET 1 P 2 HIS F 27 ASP F 34 0 SHEET 2 P 2 CYS F 51 GLY F 58 -1 N GLY F 58 O HIS F 27 SHEET 1 Q 3 ILE F 46 LYS F 48 0 SHEET 2 Q 3 GLU F 73 ILE F 83 -1 N ILE F 83 O ILE F 46 SHEET 3 Q 3 HIS F 90 HIS F 99 -1 N GLN F 98 O SER F 74 SHEET 1 R 2 LEU F 66 GLU F 72 0 SHEET 2 R 2 LYS F 101 PRO F 106 -1 N ARG F 105 O GLU F 67 SHEET 1 S 2 HIS G 27 ASP G 34 0 SHEET 2 S 2 CYS G 51 GLY G 58 -1 N GLY G 58 O HIS G 27 SHEET 1 T 3 ILE G 46 LYS G 48 0 SHEET 2 T 3 GLU G 73 ILE G 83 -1 N ILE G 83 O ILE G 46 SHEET 3 T 3 GLN G 89 HIS G 99 -1 N GLN G 98 O SER G 74 SHEET 1 U 2 LEU G 66 GLU G 72 0 SHEET 2 U 2 LYS G 101 PRO G 106 -1 N ARG G 105 O GLU G 67 SHEET 1 V 2 HIS H 27 ASP H 34 0 SHEET 2 V 2 CYS H 51 GLY H 58 -1 N GLY H 58 O HIS H 27 SHEET 1 W 3 ILE H 46 LYS H 48 0 SHEET 2 W 3 GLU H 73 ILE H 83 -1 N ILE H 83 O ILE H 46 SHEET 3 W 3 GLN H 89 HIS H 99 -1 N GLN H 98 O SER H 74 SHEET 1 X 2 LEU H 66 GLU H 72 0 SHEET 2 X 2 LYS H 101 PRO H 106 -1 N ARG H 105 O GLU H 67 SSBOND 1 CYS A 26 CYS A 68 1555 1555 2.05 SSBOND 2 CYS A 51 CYS B 60 1555 1555 2.09 SSBOND 3 CYS A 57 CYS A 102 1555 1555 2.04 SSBOND 4 CYS A 60 CYS B 51 1555 1555 2.14 SSBOND 5 CYS A 61 CYS A 104 1555 1555 2.09 SSBOND 6 CYS B 26 CYS B 68 1555 1555 2.07 SSBOND 7 CYS B 57 CYS B 102 1555 1555 2.03 SSBOND 8 CYS B 61 CYS B 104 1555 1555 2.06 SSBOND 9 CYS C 26 CYS C 68 1555 1555 2.04 SSBOND 10 CYS C 51 CYS D 60 1555 1555 2.07 SSBOND 11 CYS C 57 CYS C 102 1555 1555 2.02 SSBOND 12 CYS C 60 CYS D 51 1555 1555 2.09 SSBOND 13 CYS C 61 CYS C 104 1555 1555 2.04 SSBOND 14 CYS D 26 CYS D 68 1555 1555 2.03 SSBOND 15 CYS D 57 CYS D 102 1555 1555 2.03 SSBOND 16 CYS D 61 CYS D 104 1555 1555 2.04 SSBOND 17 CYS E 26 CYS E 68 1555 1555 2.05 SSBOND 18 CYS E 51 CYS F 60 1555 1555 2.08 SSBOND 19 CYS E 57 CYS E 102 1555 1555 2.07 SSBOND 20 CYS E 60 CYS F 51 1555 1555 2.12 SSBOND 21 CYS E 61 CYS E 104 1555 1555 2.08 SSBOND 22 CYS F 26 CYS F 68 1555 1555 2.02 SSBOND 23 CYS F 57 CYS F 102 1555 1555 2.02 SSBOND 24 CYS F 61 CYS F 104 1555 1555 2.12 SSBOND 25 CYS G 26 CYS G 68 1555 1555 2.03 SSBOND 26 CYS G 51 CYS H 60 1555 1555 2.05 SSBOND 27 CYS G 57 CYS G 102 1555 1555 2.00 SSBOND 28 CYS G 61 CYS G 104 1555 1555 2.06 SSBOND 29 CYS H 26 CYS H 68 1555 1555 2.07 SSBOND 30 CYS H 57 CYS H 102 1555 1555 2.03 SSBOND 31 CYS H 61 CYS H 104 1555 1555 2.15 CISPEP 1 LYS A 48 PRO A 49 0 0.81 CISPEP 2 LYS B 48 PRO B 49 0 -13.79 CISPEP 3 LYS C 48 PRO C 49 0 -2.48 CISPEP 4 LYS D 48 PRO D 49 0 -4.22 CISPEP 5 LYS E 48 PRO E 49 0 -11.06 CISPEP 6 LYS F 48 PRO F 49 0 -3.96 CISPEP 7 LYS G 48 PRO G 49 0 -5.66 CISPEP 8 LYS H 48 PRO H 49 0 -8.30 CRYST1 45.470 68.470 85.820 105.44 93.71 101.49 P 1 8 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 0.021993 0.004470 0.002819 0.00000 SCALE2 0.000000 0.014904 0.004438 0.00000 SCALE3 0.000000 0.000000 0.012184 0.00000 MTRIX1 1 -0.343210 -0.523640 -0.779740 -1.08611 1 MTRIX2 1 -0.532220 -0.575610 0.620820 0.54147 1 MTRIX3 1 -0.773910 0.628070 -0.081140 -1.18720 1 MTRIX1 2 0.002870 -0.220000 -0.975500 62.53261 1 MTRIX2 2 0.476400 0.857980 -0.192100 -0.08027 1 MTRIX3 2 0.879220 -0.464180 0.107270 5.22423 1 MTRIX1 3 -0.917360 0.016580 0.397700 -29.25429 1 MTRIX2 3 0.274280 -0.697740 0.661760 -26.73726 1 MTRIX3 3 0.288470 0.716150 0.635540 -49.50043 1 MTRIX1 4 0.361410 0.270470 0.892320 -41.65716 1 MTRIX2 4 0.257300 -0.948780 0.183370 -19.30638 1 MTRIX3 4 0.896200 0.163320 -0.412480 5.22588 1 MTRIX1 5 -0.954620 0.290080 -0.067500 18.67854 1 MTRIX2 5 0.210430 0.496580 -0.842100 37.36586 1 MTRIX3 5 -0.210750 -0.818090 -0.535080 18.51475 1 MTRIX1 6 0.869230 -0.466800 -0.162920 -3.92029 1 MTRIX2 6 -0.468690 -0.882880 0.029030 36.54798 1 MTRIX3 6 -0.157390 0.051120 -0.986210 22.71535 1 MTRIX1 7 0.095350 0.603750 0.791450 -37.17354 1 MTRIX2 7 -0.322050 0.771030 -0.549360 -2.72744 1 MTRIX3 7 -0.941910 -0.202510 0.267950 21.84720 1