HEADER IMMUNE SYSTEM 10-JUL-04 1TZI TITLE CRYSTAL STRUCTURE OF THE FAB YADS2 COMPLEXED WITH H-VEGF COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAB YADS2 LIGHT CHAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB YADS2 HEAVY CHAIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 11 CHAIN: V; COMPND 12 SYNONYM: VEGF-A, VASCULAR PERMEABILITY FACTOR, VPF, H-VEGF; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: 16C9; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: F0771-B6; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 12 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: 16C9; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: F0771-B6; SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_COMMON: HUMAN; SOURCE 22 ORGANISM_TAXID: 9606; SOURCE 23 GENE: VEGF, VEGFA; SOURCE 24 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 25 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHAGE DISPLAY, ANTIBODY LIBRARY, PROTEIN ENGINEERING, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR F.A.FELLOUSE,C.WIESMANN,S.S.SIDHU REVDAT 5 06-NOV-24 1TZI 1 REMARK REVDAT 4 23-AUG-23 1TZI 1 REMARK REVDAT 3 13-JUL-11 1TZI 1 VERSN REVDAT 2 24-FEB-09 1TZI 1 VERSN REVDAT 1 31-AUG-04 1TZI 0 JRNL AUTH F.A.FELLOUSE,C.WIESMANN,S.S.SIDHU JRNL TITL SYNTHETIC ANTIBODIES FROM A FOUR-AMINO-ACID CODE: A DOMINANT JRNL TITL 2 ROLE FOR TYROSINE IN ANTIGEN RECOGNITION JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 12467 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 15306681 JRNL DOI 10.1073/PNAS.0401786101 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.S.SIDHU,B.LI,Y.CHEN,F.A.FELLOUSE,C.EIGENBROT,G.FUH REMARK 1 TITL PHAGE-DISPLAYED ANTIBODY LIBRARIES OF SYNTHETIC HEAVY CHAIN REMARK 1 TITL 2 COMPLEMENTARITY DETERMINING REGIONS REMARK 1 REF J.MOL.BIOL. V. 338 299 2004 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 19702 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1023 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 25 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.86 REMARK 3 REFLECTION IN BIN (WORKING SET) : 965 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4077 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.87000 REMARK 3 B22 (A**2) : 1.62000 REMARK 3 B33 (A**2) : 7.25000 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): 0.685 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.332 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.299 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.331 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4180 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3602 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5685 ; 1.334 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8459 ; 0.945 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 530 ; 7.592 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 628 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4672 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 817 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 766 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4141 ; 0.224 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2582 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 55 ; 0.134 ; 0.200 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): 8 ; 0.342 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 71 ; 0.208 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.175 ; 0.200 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): 2656 ; 3.211 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4294 ; 5.231 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1524 ; 2.869 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1391 ; 4.696 ; 5.000 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): 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 : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 109 REMARK 3 ORIGIN FOR THE GROUP (A): 41.4673 41.7638 16.5588 REMARK 3 T TENSOR REMARK 3 T11: 0.3291 T22: 0.2785 REMARK 3 T33: 0.3541 T12: -0.1912 REMARK 3 T13: -0.0865 T23: 0.1565 REMARK 3 L TENSOR REMARK 3 L11: 6.5056 L22: 3.7384 REMARK 3 L33: 1.0625 L12: 0.3282 REMARK 3 L13: -1.2943 L23: 0.1317 REMARK 3 S TENSOR REMARK 3 S11: 0.3033 S12: -0.9396 S13: -0.6390 REMARK 3 S21: 0.5326 S22: -0.4492 S23: -0.5369 REMARK 3 S31: 0.1674 S32: 0.1218 S33: 0.1459 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 110 A 213 REMARK 3 ORIGIN FOR THE GROUP (A): 75.0629 50.9724 3.8372 REMARK 3 T TENSOR REMARK 3 T11: 0.1636 T22: 0.4500 REMARK 3 T33: 0.2798 T12: 0.0865 REMARK 3 T13: -0.0948 T23: -0.0211 REMARK 3 L TENSOR REMARK 3 L11: 6.0887 L22: 5.9477 REMARK 3 L33: 1.2189 L12: 1.6787 REMARK 3 L13: -1.0076 L23: 0.7641 REMARK 3 S TENSOR REMARK 3 S11: -0.1119 S12: -0.7766 S13: -0.3798 REMARK 3 S21: -0.2469 S22: 0.2676 S23: -0.1874 REMARK 3 S31: 0.1994 S32: 0.8518 S33: -0.1556 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 121 REMARK 3 ORIGIN FOR THE GROUP (A): 36.6517 63.0872 10.9753 REMARK 3 T TENSOR REMARK 3 T11: 0.3471 T22: 0.2617 REMARK 3 T33: 0.0696 T12: -0.0732 REMARK 3 T13: 0.1123 T23: -0.1080 REMARK 3 L TENSOR REMARK 3 L11: 6.8210 L22: 5.1979 REMARK 3 L33: 1.3479 L12: 2.5721 REMARK 3 L13: 0.5539 L23: 0.7661 REMARK 3 S TENSOR REMARK 3 S11: 0.4906 S12: -0.3658 S13: 0.3156 REMARK 3 S21: 0.2345 S22: -0.5014 S23: 0.4575 REMARK 3 S31: -0.0704 S32: 0.0094 S33: 0.0109 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 122 B 215 REMARK 3 ORIGIN FOR THE GROUP (A): 64.2039 56.9371 -5.8362 REMARK 3 T TENSOR REMARK 3 T11: 0.2934 T22: 0.2058 REMARK 3 T33: 0.2468 T12: 0.0806 REMARK 3 T13: -0.0867 T23: -0.0282 REMARK 3 L TENSOR REMARK 3 L11: 4.1881 L22: 4.5481 REMARK 3 L33: 2.8093 L12: -0.3574 REMARK 3 L13: -1.6383 L23: 2.5602 REMARK 3 S TENSOR REMARK 3 S11: 0.0245 S12: 0.0944 S13: -0.1535 REMARK 3 S21: -0.3304 S22: -0.0425 S23: 0.2049 REMARK 3 S31: -0.1479 S32: 0.2274 S33: 0.0180 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : V 13 V 109 REMARK 3 ORIGIN FOR THE GROUP (A): 1.0525 53.2817 37.3582 REMARK 3 T TENSOR REMARK 3 T11: 0.0239 T22: 0.4973 REMARK 3 T33: 0.3085 T12: 0.0819 REMARK 3 T13: 0.0013 T23: 0.1328 REMARK 3 L TENSOR REMARK 3 L11: 6.3423 L22: 0.5995 REMARK 3 L33: 6.3566 L12: 0.8842 REMARK 3 L13: -5.4427 L23: -1.1858 REMARK 3 S TENSOR REMARK 3 S11: -0.2306 S12: -1.0282 S13: -0.8947 REMARK 3 S21: -0.0424 S22: -0.1753 S23: 0.0715 REMARK 3 S31: 0.1204 S32: 1.1645 S33: 0.4058 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1TZI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000023056. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20861 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 97.3 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : 0.07600 REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.9 REMARK 200 DATA REDUNDANCY IN SHELL : 83.20 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : 0.40000 REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: THE VEGF IS FROM PDB ENTRY 1VPF. THE FAB IS FROM REMARK 200 AN IN-HOUSE DETERMINED STRUCTURE. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM CHLORIDE, PEG 6000, MES, PH REMARK 280 6.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.71050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.71050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 48.25200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 74.79400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 48.25200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 74.79400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.71050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 48.25200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 74.79400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.71050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 48.25200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 74.79400 REMARK 290 SMTRY3 8 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 300 REMARK: FOR VEGF, THE BIOLOGICAL ASSEMBLY CORRESPONDS TO TWO COPIES REMARK 300 OF CHAIN V, RELATED BY A TWO FOLD SYMETRY AND PHYSICALLY LINKED BY REMARK 300 A DISULFIDE BRIDGE. THE FAB VEGF COMPLEX, THE BIOLOGICAL ASSEMBLY REMARK 300 CORRESPONDS TO ALL CHAINS, RELATED BY A TWO FOLD SYMETRY. 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, V 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 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 58.71050 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 V 8 REMARK 465 GLN V 9 REMARK 465 ASN V 10 REMARK 465 HIS V 11 REMARK 465 HIS V 12 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 1 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP V 19 CB - CG - OD2 ANGL. DEV. = 5.8 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 SER A 26 -160.48 -69.79 REMARK 500 TYR A 29 -108.78 -5.89 REMARK 500 ALA A 30 91.88 58.69 REMARK 500 ALA A 32 42.87 -90.09 REMARK 500 LEU A 47 -60.68 -120.92 REMARK 500 ASP A 50 14.55 43.74 REMARK 500 ALA A 51 -33.29 94.47 REMARK 500 ALA A 84 -179.77 -178.35 REMARK 500 GLN A 89 113.81 -162.04 REMARK 500 ASP A 96 27.08 -64.70 REMARK 500 ASN A 138 79.18 55.08 REMARK 500 ALA A 144 134.64 -177.11 REMARK 500 ASN A 152 9.22 58.82 REMARK 500 LEU A 154 137.97 -39.79 REMARK 500 GLN A 160 127.83 -170.61 REMARK 500 THR A 164 138.39 -36.36 REMARK 500 LEU A 201 88.74 -161.45 REMARK 500 PRO A 204 98.91 -39.33 REMARK 500 PHE B 27 152.73 175.19 REMARK 500 TYR B 99 35.66 -98.13 REMARK 500 ALA B 100A -5.26 67.69 REMARK 500 ASP B 144 86.67 66.94 REMARK 500 PHE B 146 143.58 -176.99 REMARK 500 PRO B 147 -160.40 -72.27 REMARK 500 ASN B 155 50.11 28.20 REMARK 500 PRO B 213 -171.51 -52.29 REMARK 500 CYS V 26 108.45 -21.89 REMARK 500 GLU V 44 29.60 -77.53 REMARK 500 ASP V 63 147.40 169.48 REMARK 500 SER V 74 129.51 -173.46 REMARK 500 HIS V 86 -3.58 87.42 REMARK 500 GLN V 87 -77.45 -112.19 REMARK 500 LYS V 108 103.45 -55.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR V 39 PRO V 40 -148.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TZH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE FAB YADS1 COMPLEXED WITH H-VEGF REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHORS INFORMED THAT THE SEQUENCES OF FAB YADS2 LIGHT REMARK 999 CHAIN AND FAB YADS2 HEAVY CHAIN ARE NOT YET AVAILABLE IN REMARK 999 ANY REFERENCE SEQUENCE DATABASE. DBREF 1TZI V 8 109 UNP P15692 VEGFA_HUMAN 34 135 DBREF 1TZI A 1 214 PDB 1TZI 1TZI 1 214 DBREF 1TZI B 1 215 PDB 1TZI 1TZI 1 215 SEQRES 1 A 214 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 A 214 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 A 214 GLN SER TYR ALA TYR ALA VAL ALA TRP TYR GLN GLN LYS SEQRES 4 A 214 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ASP ALA SER SEQRES 5 A 214 TYR LEU TYR SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 A 214 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 A 214 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN ALA SEQRES 8 A 214 TYR SER SER PRO ASP THR PHE GLY GLN GLY THR LYS VAL SEQRES 9 A 214 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 A 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 A 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 A 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 A 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 A 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 A 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 A 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 A 214 PHE ASN ARG GLY GLU CYS SEQRES 1 B 222 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 222 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 222 PHE ALA ILE TYR ASP TYR ASP ILE HIS TRP VAL ARG GLN SEQRES 4 B 222 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA ASP ILE ALA SEQRES 5 B 222 PRO TYR ALA GLY ALA THR ALA TYR ALA ASP SER VAL LYS SEQRES 6 B 222 GLY ARG PHE THR ILE SER ALA ASP THR SER LYS ASN THR SEQRES 7 B 222 ALA TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 B 222 ALA VAL TYR TYR CYS SER ARG SER SER TYR ALA TYR TYR SEQRES 9 B 222 ALA ALA MET ASP TYR TRP GLY GLN GLY THR LEU VAL THR SEQRES 10 B 222 VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO SEQRES 11 B 222 LEU ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA SEQRES 12 B 222 ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO SEQRES 13 B 222 VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY SEQRES 14 B 222 VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU SEQRES 15 B 222 TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER SER SEQRES 16 B 222 LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS SEQRES 17 B 222 PRO SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SEQRES 18 B 222 SER SEQRES 1 V 102 GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP VAL SEQRES 2 V 102 TYR GLN ARG SER TYR CYS HIS PRO ILE GLU THR LEU VAL SEQRES 3 V 102 ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE SEQRES 4 V 102 PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY GLY SEQRES 5 V 102 CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR GLU SEQRES 6 V 102 GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS PRO SEQRES 7 V 102 HIS GLN GLY GLN HIS ILE GLY GLU MET SER PHE LEU GLN SEQRES 8 V 102 HIS ASN LYS CYS GLU CYS ARG PRO LYS LYS ASP HELIX 1 1 SER A 121 GLY A 128 1 8 HELIX 2 2 LYS A 183 LYS A 188 1 6 HELIX 3 3 ARG B 83 THR B 87 5 5 HELIX 4 4 SER B 127 LYS B 129 5 3 HELIX 5 5 SER B 156 ALA B 158 5 3 HELIX 6 6 LYS B 201 ASN B 204 5 4 HELIX 7 7 LYS V 16 TYR V 25 1 10 HELIX 8 8 ILE V 35 TYR V 39 1 5 SHEET 1 A 6 SER A 10 SER A 14 0 SHEET 2 A 6 THR A 102 LYS A 107 1 O LYS A 103 N LEU A 11 SHEET 3 A 6 ALA A 84 GLN A 90 -1 N ALA A 84 O VAL A 104 SHEET 4 A 6 VAL A 33 GLN A 38 -1 N TYR A 36 O TYR A 87 SHEET 5 A 6 LYS A 45 TYR A 49 -1 O LYS A 45 N GLN A 37 SHEET 6 A 6 TYR A 53 LEU A 54 -1 O TYR A 53 N TYR A 49 SHEET 1 B 3 VAL A 19 ARG A 24 0 SHEET 2 B 3 ASP A 70 ILE A 75 -1 O PHE A 71 N CYS A 23 SHEET 3 B 3 PHE A 62 SER A 67 -1 N SER A 63 O THR A 74 SHEET 1 C 4 SER A 114 PHE A 118 0 SHEET 2 C 4 THR A 129 PHE A 139 -1 O ASN A 137 N SER A 114 SHEET 3 C 4 TYR A 173 SER A 182 -1 O LEU A 179 N VAL A 132 SHEET 4 C 4 GLU A 161 VAL A 163 -1 N SER A 162 O SER A 176 SHEET 1 D 4 ALA A 153 LEU A 154 0 SHEET 2 D 4 LYS A 145 VAL A 150 -1 N VAL A 150 O ALA A 153 SHEET 3 D 4 VAL A 191 HIS A 198 -1 O THR A 197 N LYS A 145 SHEET 4 D 4 LEU A 201 ASN A 210 -1 O PHE A 209 N TYR A 192 SHEET 1 E 4 GLN B 3 SER B 7 0 SHEET 2 E 4 LEU B 18 SER B 25 -1 O ALA B 23 N VAL B 5 SHEET 3 E 4 THR B 77 MET B 82 -1 O LEU B 80 N LEU B 20 SHEET 4 E 4 THR B 68 ASP B 72 -1 N ASP B 72 O THR B 77 SHEET 1 F 6 LEU B 11 VAL B 12 0 SHEET 2 F 6 THR B 107 VAL B 111 1 O THR B 110 N VAL B 12 SHEET 3 F 6 ALA B 88 SER B 95 -1 N ALA B 88 O VAL B 109 SHEET 4 F 6 ASP B 33 GLN B 39 -1 N VAL B 37 O TYR B 91 SHEET 5 F 6 GLU B 46 ALA B 52 -1 O ILE B 51 N ILE B 34 SHEET 6 F 6 ALA B 56 TYR B 59 -1 O ALA B 58 N ASP B 50 SHEET 1 G 4 LEU B 11 VAL B 12 0 SHEET 2 G 4 THR B 107 VAL B 111 1 O THR B 110 N VAL B 12 SHEET 3 G 4 ALA B 88 SER B 95 -1 N ALA B 88 O VAL B 109 SHEET 4 G 4 MET B 100C TRP B 103 -1 O ASP B 101 N ARG B 94 SHEET 1 H 4 SER B 120 LEU B 124 0 SHEET 2 H 4 THR B 135 TYR B 145 -1 O LEU B 141 N PHE B 122 SHEET 3 H 4 TYR B 176 PRO B 185 -1 O LEU B 178 N VAL B 142 SHEET 4 H 4 VAL B 163 THR B 165 -1 N HIS B 164 O VAL B 181 SHEET 1 I 4 THR B 131 SER B 132 0 SHEET 2 I 4 THR B 135 TYR B 145 -1 O THR B 135 N SER B 132 SHEET 3 I 4 TYR B 176 PRO B 185 -1 O LEU B 178 N VAL B 142 SHEET 4 I 4 VAL B 169 LEU B 170 -1 N VAL B 169 O SER B 177 SHEET 1 J 3 THR B 151 TRP B 154 0 SHEET 2 J 3 ILE B 195 HIS B 200 -1 O ASN B 197 N SER B 153 SHEET 3 J 3 THR B 205 LYS B 210 -1 O THR B 205 N HIS B 200 SHEET 1 K 2 HIS V 27 ASP V 34 0 SHEET 2 K 2 CYS V 51 GLY V 58 -1 O LEU V 54 N THR V 31 SHEET 1 L 3 ILE V 46 LYS V 48 0 SHEET 2 L 3 LEU V 66 LYS V 84 -1 O ILE V 83 N ILE V 46 SHEET 3 L 3 GLY V 88 PRO V 106 -1 O GLY V 88 N LYS V 84 SSBOND 1 CYS A 23 CYS A 88 1555 1555 2.04 SSBOND 2 CYS A 134 CYS A 194 1555 1555 2.02 SSBOND 3 CYS B 22 CYS B 92 1555 1555 2.06 SSBOND 4 CYS B 140 CYS B 196 1555 1555 2.01 SSBOND 5 CYS V 26 CYS V 68 1555 1555 2.02 SSBOND 6 CYS V 51 CYS V 60 1555 3555 2.91 SSBOND 7 CYS V 57 CYS V 102 1555 1555 2.04 SSBOND 8 CYS V 61 CYS V 104 1555 1555 2.02 CISPEP 1 SER A 7 PRO A 8 0 -6.98 CISPEP 2 TYR A 140 PRO A 141 0 2.82 CISPEP 3 ARG A 211 GLY A 212 0 -6.18 CISPEP 4 GLU A 213 CYS A 214 0 0.77 CISPEP 5 PHE B 146 PRO B 147 0 -9.46 CISPEP 6 GLU B 148 PRO B 149 0 -3.47 CISPEP 7 LYS V 48 PRO V 49 0 -8.06 CRYST1 96.504 149.588 117.421 90.00 90.00 90.00 C 2 2 21 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 0.010362 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006685 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008516 0.00000