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 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END