HEADER HORMONE 15-NOV-07 3BDY TITLE DUAL SPECIFIC BH1 FAB IN COMPLEX WITH VEGF COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAB FRAGMENT -HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB FRAGMENT -LIGHT CHAIN; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 11 CHAIN: V; COMPND 12 FRAGMENT: SEQUENCE DATABASE RESIDUES 27-135; COMPND 13 SYNONYM: VEGF-A, VASCULAR PERMEABILITY FACTOR, VPF; COMPND 14 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 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 GENE: VEGF, VEGFA; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FAB COMPLEX, ANGIOGENESIS, DEVELOPMENTAL PROTEIN, DIFFERENTIATION, KEYWDS 2 GLYCOPROTEIN, GROWTH FACTOR, HEPARIN-BINDING, MITOGEN, SECRETED, KEYWDS 3 HORMONE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.BOSTROM,C.WIESMANN,B.A.APPLETON REVDAT 6 30-AUG-23 3BDY 1 REMARK DBREF REVDAT 5 25-OCT-17 3BDY 1 REMARK REVDAT 4 13-JUL-11 3BDY 1 VERSN REVDAT 3 31-MAR-09 3BDY 1 JRNL REVDAT 2 24-FEB-09 3BDY 1 VERSN REVDAT 1 18-NOV-08 3BDY 0 JRNL AUTH J.BOSTROM,S.F.YU,D.KAN,B.A.APPLETON,C.V.LEE,K.BILLECI,W.MAN, JRNL AUTH 2 F.PEALE,S.ROSS,C.WIESMANN,G.FUH JRNL TITL VARIANTS OF THE ANTIBODY HERCEPTIN THAT INTERACT WITH HER2 JRNL TITL 2 AND VEGF AT THE ANTIGEN BINDING SITE JRNL REF SCIENCE V. 323 1610 2009 JRNL REFN ISSN 0036-8075 JRNL PMID 19299620 JRNL DOI 10.1126/SCIENCE.1165480 REMARK 2 REMARK 2 RESOLUTION. 2.60 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 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 24225 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1248 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.65 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1340 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.4130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4072 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 47 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) : 40.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.01000 REMARK 3 B22 (A**2) : -0.56000 REMARK 3 B33 (A**2) : 1.58000 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): 0.410 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.283 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.194 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.206 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4184 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2829 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5688 ; 1.255 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6899 ; 0.805 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 524 ; 6.122 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;37.833 ;24.220 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 674 ;15.219 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;15.435 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 624 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4644 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 826 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 607 ; 0.185 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2648 ; 0.190 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1943 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2298 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 98 ; 0.127 ; 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): 12 ; 0.346 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 30 ; 0.140 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.075 ; 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): 3373 ; 2.769 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1063 ; 0.517 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4260 ; 3.645 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1871 ; 2.670 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1428 ; 3.823 ; 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 : H 0 H 115 REMARK 3 ORIGIN FOR THE GROUP (A): -25.4998 -52.3042 1.7867 REMARK 3 T TENSOR REMARK 3 T11: -0.2637 T22: -0.1109 REMARK 3 T33: -0.2229 T12: -0.0369 REMARK 3 T13: -0.0034 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 3.8860 L22: 3.7232 REMARK 3 L33: 2.0411 L12: 0.6662 REMARK 3 L13: 1.1764 L23: -0.3963 REMARK 3 S TENSOR REMARK 3 S11: 0.0087 S12: -0.2249 S13: 0.1224 REMARK 3 S21: 0.1727 S22: -0.0860 S23: 0.0037 REMARK 3 S31: -0.0941 S32: 0.1319 S33: 0.0773 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 : H 116 H 215 REMARK 3 ORIGIN FOR THE GROUP (A): -45.5629 -27.6691 6.8947 REMARK 3 T TENSOR REMARK 3 T11: 0.2365 T22: 0.0986 REMARK 3 T33: -0.1399 T12: 0.0188 REMARK 3 T13: -0.0386 T23: -0.1095 REMARK 3 L TENSOR REMARK 3 L11: 8.8573 L22: 4.8558 REMARK 3 L33: 2.6832 L12: 0.0200 REMARK 3 L13: 0.3558 L23: 0.1268 REMARK 3 S TENSOR REMARK 3 S11: -0.0486 S12: -1.3177 S13: 0.1570 REMARK 3 S21: 0.9493 S22: 0.0889 S23: -0.1741 REMARK 3 S31: -0.3100 S32: -0.4198 S33: -0.0403 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 : L 1 L 109 REMARK 3 ORIGIN FOR THE GROUP (A): -43.4596 -58.8465 -10.6603 REMARK 3 T TENSOR REMARK 3 T11: -0.2283 T22: -0.1765 REMARK 3 T33: -0.2066 T12: -0.0530 REMARK 3 T13: 0.0169 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 4.4846 L22: 1.2973 REMARK 3 L33: 1.4973 L12: -0.8890 REMARK 3 L13: 1.1810 L23: -0.3277 REMARK 3 S TENSOR REMARK 3 S11: 0.0087 S12: 0.1869 S13: -0.1329 REMARK 3 S21: -0.0295 S22: 0.0113 S23: 0.0392 REMARK 3 S31: 0.0637 S32: -0.0473 S33: -0.0200 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 : L 110 L 213 REMARK 3 ORIGIN FOR THE GROUP (A): -52.8848 -21.8276 -6.5557 REMARK 3 T TENSOR REMARK 3 T11: 0.1654 T22: -0.0806 REMARK 3 T33: 0.0534 T12: 0.0607 REMARK 3 T13: 0.0316 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 5.7254 L22: 6.7518 REMARK 3 L33: 2.6788 L12: 2.7456 REMARK 3 L13: 1.2566 L23: 0.7894 REMARK 3 S TENSOR REMARK 3 S11: -0.4113 S12: 0.2746 S13: 1.0980 REMARK 3 S21: 0.2808 S22: 0.3532 S23: 0.2070 REMARK 3 S31: -0.9660 S32: -0.1375 S33: 0.0581 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 14 V 108 REMARK 3 ORIGIN FOR THE GROUP (A): -33.1874 -95.9046 -7.6920 REMARK 3 T TENSOR REMARK 3 T11: 0.3551 T22: -0.0513 REMARK 3 T33: 0.2601 T12: 0.0473 REMARK 3 T13: -0.0175 T23: -0.0999 REMARK 3 L TENSOR REMARK 3 L11: 0.3596 L22: 9.1840 REMARK 3 L33: 1.1560 L12: 0.8805 REMARK 3 L13: -0.4052 L23: -3.2093 REMARK 3 S TENSOR REMARK 3 S11: -0.1310 S12: 0.0398 S13: -0.1964 REMARK 3 S21: -1.3429 S22: 0.0132 S23: -0.0483 REMARK 3 S31: 0.6267 S32: 0.0130 S33: 0.1178 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 3BDY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000045399. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24705 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.65800 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1N8Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: FOR CRYSTALLIZATION OF THE FAB/VEGF (8 REMARK 280 -109) COMPLEX, EQUAL VOLUMES OF PROTEIN COMPLEX SOLUTION (10.6 REMARK 280 MG/ML PROTEIN, 300 MM NACL, 25 MM TRIS-HCL PH 7.5) AND REMARK 280 CRYSTALLIZATION BUFFER CONTAINING 0.15 D, L MALIC ACID PH 7.0, REMARK 280 20% PEG3350 WERE MIXED AND EQUILIBRATED AT 19 C. PRIOR TO DATA REMARK 280 COLLECTION THE CRYSTALS WERE CRYO-PROTECTED BY TRANSFER BETWEEN REMARK 280 DROPS CONTAINING 5%, 10% AND 15% GLYCEROL IN ARTIFICIAL MOTHER REMARK 280 LIQUOR, FOLLOWED BY FLASH FREEZE IN LIQUID NITROGEN, VAPOR REMARK 280 DIFFUSION, 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 38.82500 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 38.82500 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 50.30000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 98.98900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 50.30000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 98.98900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.82500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 50.30000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 98.98900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.82500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 50.30000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 98.98900 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 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: 3460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L 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: 2720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 -197.97800 REMARK 350 BIOMT3 2 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 GLU H -2 REMARK 465 ILE H -1 REMARK 465 LYS H 131 REMARK 465 SER H 132 REMARK 465 THR H 133 REMARK 465 SER H 134 REMARK 465 GLY H 135 REMARK 465 LYS H 216 REMARK 465 SER H 217 REMARK 465 CYS H 218 REMARK 465 ASP H 219 REMARK 465 LYS H 220 REMARK 465 THR H 221 REMARK 465 HIS H 222 REMARK 465 CYS L 214 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 465 GLU V 13 REMARK 465 ASP V 109 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS H 92 CB CYS H 92 SG -0.109 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 ASN H 206 47.44 38.00 REMARK 500 SER L 77 86.71 -156.47 REMARK 500 ALA L 84 171.19 175.36 REMARK 500 ASN L 138 72.61 53.30 REMARK 500 ASN L 152 -11.55 73.18 REMARK 500 LYS L 190 -64.38 -103.41 REMARK 500 ARG L 211 93.79 -67.68 REMARK 500 CYS V 26 104.67 -18.95 REMARK 500 GLU V 42 81.21 -62.08 REMARK 500 GLN V 87 -57.34 -127.49 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 GOL L 215 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BE1 RELATED DB: PDB DBREF 3BDY H -2 222 PDB 3BDY 3BDY -2 222 DBREF 3BDY L 1 214 PDB 3BDY 3BDY 1 214 DBREF 3BDY V 8 109 UNP P15692 VEGFA_HUMAN 34 135 SEQRES 1 H 230 GLU ILE SER GLU VAL GLN LEU VAL GLU SER GLY GLY GLY SEQRES 2 H 230 LEU VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA SEQRES 3 H 230 ALA SER GLY PHE ASN ILE LYS ASP THR TYR ILE HIS TRP SEQRES 4 H 230 VAL ARG GLN ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA SEQRES 5 H 230 ARG ILE TYR PRO THR ASN GLY TYR THR ARG TYR ALA ASP SEQRES 6 H 230 SER VAL LYS GLY ARG PHE THR ILE SER ALA ASP THR SER SEQRES 7 H 230 LYS ASN THR ALA TYR LEU GLN MET ASN SER LEU ARG ALA SEQRES 8 H 230 GLU ASP THR ALA VAL TYR TYR CYS SER ARG TRP GLY GLY SEQRES 9 H 230 ASP GLY PHE TYR ALA MET ASP TYR TRP GLY GLN GLY THR SEQRES 10 H 230 LEU VAL THR VAL SER SER ALA SER THR LYS GLY PRO SER SEQRES 11 H 230 VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY SEQRES 12 H 230 GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE SEQRES 13 H 230 PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU SEQRES 14 H 230 THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SEQRES 15 H 230 SER GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SEQRES 16 H 230 SER SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL SEQRES 17 H 230 ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL SEQRES 18 H 230 GLU PRO LYS SER CYS ASP LYS THR HIS SEQRES 1 L 218 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 218 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 218 GLN ASP ILE PRO ARG SER ILE SER GLY TYR VAL ALA TRP SEQRES 4 L 218 TYR GLN GLN LYS PRO GLY LYS ALA PRO LYS LEU LEU ILE SEQRES 5 L 218 TYR TRP GLY SER TYR LEU TYR SER GLY VAL PRO SER ARG SEQRES 6 L 218 PHE SER GLY SER GLY SER GLY THR ASP PHE THR LEU THR SEQRES 7 L 218 ILE SER SER LEU GLN PRO GLU ASP PHE ALA THR TYR TYR SEQRES 8 L 218 CYS GLN GLN HIS TYR THR THR PRO PRO THR PHE GLY GLN SEQRES 9 L 218 GLY THR LYS VAL GLU ILE LYS ARG THR VAL ALA ALA PRO SEQRES 10 L 218 SER VAL PHE ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SEQRES 11 L 218 SER GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN PHE SEQRES 12 L 218 TYR PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN SEQRES 13 L 218 ALA LEU GLN SER GLY ASN SER GLN GLU SER VAL THR GLU SEQRES 14 L 218 GLN ASP SER LYS ASP SER THR TYR SER LEU SER SER THR SEQRES 15 L 218 LEU THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS VAL SEQRES 16 L 218 TYR ALA CYS GLU VAL THR HIS GLN GLY LEU SER SER PRO SEQRES 17 L 218 VAL THR LYS SER PHE ASN ARG GLY GLU CYS 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 HET GOL L 215 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *47(H2 O) HELIX 1 1 ASN H 28 THR H 32 5 5 HELIX 2 2 ARG H 83 THR H 87 5 5 HELIX 3 3 SER H 158 ALA H 160 5 3 HELIX 4 4 SER H 189 LEU H 191 5 3 HELIX 5 5 LYS H 203 ASN H 206 5 4 HELIX 6 6 GLN L 79 PHE L 83 5 5 HELIX 7 7 SER L 121 LYS L 126 1 6 HELIX 8 8 LYS L 183 LYS L 188 1 6 HELIX 9 9 LYS V 16 SER V 24 1 9 HELIX 10 10 ILE V 35 TYR V 39 1 5 SHEET 1 A 4 GLN H 3 SER H 7 0 SHEET 2 A 4 LEU H 18 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 A 4 THR H 77 MET H 82 -1 O MET H 82 N LEU H 18 SHEET 4 A 4 PHE H 67 ASP H 72 -1 N THR H 68 O GLN H 81 SHEET 1 B 6 GLY H 10 VAL H 12 0 SHEET 2 B 6 THR H 109 VAL H 113 1 O THR H 112 N VAL H 12 SHEET 3 B 6 ALA H 88 ARG H 94 -1 N TYR H 90 O THR H 109 SHEET 4 B 6 ILE H 34 GLN H 39 -1 N HIS H 35 O SER H 93 SHEET 5 B 6 GLU H 46 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 B 6 THR H 57 TYR H 59 -1 O ARG H 58 N ARG H 50 SHEET 1 C 4 GLY H 10 VAL H 12 0 SHEET 2 C 4 THR H 109 VAL H 113 1 O THR H 112 N VAL H 12 SHEET 3 C 4 ALA H 88 ARG H 94 -1 N TYR H 90 O THR H 109 SHEET 4 C 4 TYR H 104 TRP H 105 -1 O TYR H 104 N ARG H 94 SHEET 1 D 4 SER H 122 LEU H 126 0 SHEET 2 D 4 THR H 137 TYR H 147 -1 O LEU H 143 N PHE H 124 SHEET 3 D 4 TYR H 178 PRO H 187 -1 O VAL H 186 N ALA H 138 SHEET 4 D 4 VAL H 165 THR H 167 -1 N HIS H 166 O VAL H 183 SHEET 1 E 4 SER H 122 LEU H 126 0 SHEET 2 E 4 THR H 137 TYR H 147 -1 O LEU H 143 N PHE H 124 SHEET 3 E 4 TYR H 178 PRO H 187 -1 O VAL H 186 N ALA H 138 SHEET 4 E 4 VAL H 171 LEU H 172 -1 N VAL H 171 O SER H 179 SHEET 1 F 3 THR H 153 TRP H 156 0 SHEET 2 F 3 TYR H 196 HIS H 202 -1 O ASN H 199 N SER H 155 SHEET 3 F 3 THR H 207 VAL H 213 -1 O THR H 207 N HIS H 202 SHEET 1 G 4 MET L 4 SER L 7 0 SHEET 2 G 4 VAL L 19 ALA L 25 -1 O THR L 22 N SER L 7 SHEET 3 G 4 ASP L 70 ILE L 75 -1 O ILE L 75 N VAL L 19 SHEET 4 G 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 H 6 SER L 10 SER L 14 0 SHEET 2 H 6 THR L 102 LYS L 107 1 O LYS L 107 N ALA L 13 SHEET 3 H 6 ALA L 84 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 H 6 VAL L 33 GLN L 38 -1 N TYR L 36 O TYR L 87 SHEET 5 H 6 LYS L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 H 6 TYR L 53 LEU L 54 -1 O TYR L 53 N TYR L 49 SHEET 1 I 4 SER L 10 SER L 14 0 SHEET 2 I 4 THR L 102 LYS L 107 1 O LYS L 107 N ALA L 13 SHEET 3 I 4 ALA L 84 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 I 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 J 4 ILE L 29 SER L 30 0 SHEET 2 J 4 GLY V 88 PRO V 106 -1 O ILE V 91 N SER L 30 SHEET 3 J 4 LEU V 66 LYS V 84 -1 N ILE V 76 O PHE V 96 SHEET 4 J 4 ILE V 46 LYS V 48 -1 N ILE V 46 O ILE V 83 SHEET 1 K 4 SER L 114 PHE L 118 0 SHEET 2 K 4 THR L 129 PHE L 139 -1 O ASN L 137 N SER L 114 SHEET 3 K 4 TYR L 173 SER L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 K 4 SER L 159 VAL L 163 -1 N SER L 162 O SER L 176 SHEET 1 L 4 ALA L 153 LEU L 154 0 SHEET 2 L 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 L 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 L 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SHEET 1 M 2 HIS V 27 ASP V 34 0 SHEET 2 M 2 CYS V 51 GLY V 58 -1 O LEU V 54 N THR V 31 SSBOND 1 CYS H 22 CYS H 92 1555 1555 2.00 SSBOND 2 CYS H 142 CYS H 198 1555 1555 2.02 SSBOND 3 CYS L 23 CYS L 88 1555 1555 2.07 SSBOND 4 CYS L 134 CYS L 194 1555 1555 2.02 SSBOND 5 CYS V 26 CYS V 68 1555 1555 2.03 SSBOND 6 CYS V 51 CYS V 60 1555 4545 2.47 SSBOND 7 CYS V 57 CYS V 102 1555 1555 2.04 SSBOND 8 CYS V 61 CYS V 104 1555 1555 2.04 CISPEP 1 PHE H 148 PRO H 149 0 -5.36 CISPEP 2 GLU H 150 PRO H 151 0 0.19 CISPEP 3 SER L 7 PRO L 8 0 -0.94 CISPEP 4 THR L 94 PRO L 95 0 -6.04 CISPEP 5 TYR L 140 PRO L 141 0 2.32 CISPEP 6 LYS V 48 PRO V 49 0 0.11 SITE 1 AC1 6 GLN L 37 LYS L 39 PRO L 59 ARG L 61 SITE 2 AC1 6 GLU L 81 ASP L 82 CRYST1 100.600 197.978 77.650 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 0.009940 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005051 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012878 0.00000