PDB Short entry for 1WQ8 HEADER TOXIN 23-SEP-04 1WQ8 TITLE CRYSTAL STRUCTURE OF VAMMIN, A VEGF-F FROM A SNAKE VENOM COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR TOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VR-1, VEGF-F SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIPERA ASPIS ASPIS; SOURCE 3 ORGANISM_TAXID: 194601; SOURCE 4 STRAIN: ASPIS; SOURCE 5 SECRETION: VENOM KEYWDS SNAKE VENOM, VASCULAR ENDOTHELIAL GROWTH FACTOR, VEGF, VEGF-F, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR K.SUTO,Y.YAMAZAKI,T.MORITA,H.MIZUNO REVDAT 5 03-APR-24 1WQ8 1 REMARK REVDAT 4 25-DEC-19 1WQ8 1 SEQRES LINK REVDAT 3 13-JUL-11 1WQ8 1 VERSN REVDAT 2 24-FEB-09 1WQ8 1 VERSN REVDAT 1 07-DEC-04 1WQ8 0 JRNL AUTH K.SUTO,Y.YAMAZAKI,T.MORITA,H.MIZUNO JRNL TITL CRYSTAL STRUCTURES OF NOVEL VASCULAR ENDOTHELIAL GROWTH JRNL TITL 2 FACTORS (VEGF) FROM SNAKE VENOMS: INSIGHT INTO SELECTIVE JRNL TITL 3 VEGF BINDING TO KINASE INSERT DOMAIN-CONTAINING RECEPTOR BUT JRNL TITL 4 NOT TO FMS-LIKE TYROSINE KINASE-1. JRNL REF J.BIOL.CHEM. V. 280 2126 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15542594 JRNL DOI 10.1074/JBC.M411395200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.YAMAZAKI,K.TAKANI,H.ATODA,T.MORITA REMARK 1 TITL SNAKE VENOM VASCULAR ENDOTHELIAL GROWTH FACTORS (VEGFS) REMARK 1 TITL 2 EXHIBIT POTENT ACTIVITY THROUGH THEIR SPECIFIC RECOGNITION REMARK 1 TITL 3 OF KDR (VEGF RECEPTOR 2) REMARK 1 REF J.BIOL.CHEM. V. 278 51985 2003 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 14600159 REMARK 1 DOI 10.1074/JBC.C300454200 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1706273.810 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 12885 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 SET) : 0.192 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 648 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1961 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 122 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 791 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 172 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.58000 REMARK 3 B22 (A**2) : 0.63000 REMARK 3 B33 (A**2) : -1.21000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.10 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.790 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.370 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.050 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.690 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.960 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 51.60 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : BUFFER.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : BUFFER.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WQ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000023875. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SILICON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12903 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: VR-1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, TRIS-HCL, GLYCEROL, PH 9.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 42.76300 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 42.76300 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 43.18250 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 42.76300 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 42.76300 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 43.18250 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 42.76300 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 42.76300 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 43.18250 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 42.76300 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 42.76300 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 43.18250 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 42.76300 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 42.76300 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 43.18250 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 42.76300 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 42.76300 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 43.18250 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 42.76300 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 42.76300 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 43.18250 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 42.76300 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 42.76300 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 43.18250 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE TWO FOLD AXIS:Y, X, -Z 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: 3370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 20430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 85.52600 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 85.52600 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 85.52600 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 85.52600 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 85.52600 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 85.52600 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 8 0.000000 -1.000000 0.000000 85.52600 REMARK 350 BIOMT2 8 -1.000000 0.000000 0.000000 85.52600 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1021 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1069 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1168 LIES ON A SPECIAL POSITION. 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 GLU A 101 REMARK 465 PRO A 102 REMARK 465 ASP A 103 REMARK 465 GLY A 104 REMARK 465 PRO A 105 REMARK 465 LYS A 106 REMARK 465 GLU A 107 REMARK 465 LYS A 108 REMARK 465 PRO A 109 REMARK 465 ARG A 110 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 OG SER A 12 O HOH A 1169 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 1173 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WQ9 RELATED DB: PDB REMARK 900 VR-1, A VEGF-F FROM A SNAKE VENOM DBREF 1WQ8 A 2 110 UNP P83942 TXVE_VIPAP 2 110 SEQRES 1 A 110 PCA VAL ARG PRO PHE LEU GLU VAL HIS GLU ARG SER ALA SEQRES 2 A 110 CYS GLN ALA ARG GLU THR LEU VAL PRO ILE LEU GLN GLU SEQRES 3 A 110 TYR PRO ASP GLU ILE SER ASP ILE PHE ARG PRO SER CYS SEQRES 4 A 110 VAL ALA VAL LEU ARG CYS SER GLY CYS CYS THR ASP GLU SEQRES 5 A 110 SER LEU LYS CYS THR PRO VAL GLY LYS HIS THR VAL ASP SEQRES 6 A 110 ILE GLN ILE MET ARG VAL ASN PRO ARG THR GLN SER SER SEQRES 7 A 110 LYS MET GLU VAL MET LYS PHE THR GLU HIS THR ALA CYS SEQRES 8 A 110 GLU CYS ARG PRO ARG ARG LYS GLN GLY GLU PRO ASP GLY SEQRES 9 A 110 PRO LYS GLU LYS PRO ARG MODRES 1WQ8 PCA A 1 GLN PYROGLUTAMIC ACID HET PCA A 1 8 HET TRS A1173 8 HETNAM PCA PYROGLUTAMIC ACID HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 1 PCA C5 H7 N O3 FORMUL 2 TRS C4 H12 N O3 1+ FORMUL 3 HOH *172(H2 O) HELIX 1 1 PRO A 4 ALA A 13 1 10 HELIX 2 2 ILE A 23 TYR A 27 1 5 SHEET 1 A 2 GLN A 15 PRO A 22 0 SHEET 2 A 2 CYS A 39 SER A 46 -1 O VAL A 40 N VAL A 21 SHEET 1 B 3 ILE A 34 ARG A 36 0 SHEET 2 B 3 LYS A 55 VAL A 71 -1 O VAL A 71 N ILE A 34 SHEET 3 B 3 SER A 78 ARG A 94 -1 O GLU A 92 N THR A 57 SSBOND 1 CYS A 14 CYS A 56 1555 1555 2.05 SSBOND 2 CYS A 39 CYS A 48 1555 7555 2.36 SSBOND 3 CYS A 45 CYS A 91 1555 1555 2.02 SSBOND 4 CYS A 49 CYS A 93 1555 1555 2.03 LINK C PCA A 1 N VAL A 2 1555 1555 1.33 CISPEP 1 ARG A 36 PRO A 37 0 -6.29 SITE 1 AC1 9 LEU A 20 PRO A 22 GLY A 47 CYS A 48 SITE 2 AC1 9 HOH A1008 HOH A1045 HOH A1071 HOH A1081 SITE 3 AC1 9 HOH A1118 CRYST1 85.526 85.526 86.365 90.00 90.00 90.00 I 4 2 2 16 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 0.011692 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011692 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011579 0.00000 HETATM 1 N PCA A 1 30.216 1.602 -5.105 1.00 41.84 N HETATM 2 CA PCA A 1 29.515 1.860 -6.340 1.00 39.66 C HETATM 3 CB PCA A 1 28.041 1.782 -5.953 1.00 40.53 C HETATM 4 CG PCA A 1 28.048 1.356 -4.498 1.00 44.10 C HETATM 5 CD PCA A 1 29.474 1.325 -4.080 1.00 44.65 C HETATM 6 OE PCA A 1 29.915 1.077 -2.941 1.00 47.87 O HETATM 7 C PCA A 1 29.924 3.223 -6.874 1.00 36.45 C HETATM 8 O PCA A 1 29.983 4.201 -6.126 1.00 38.26 O