HEADER SIGNALING PROTEIN 17-JUN-20 6ZFL TITLE HIGH RESOLUTION STRUCTURE OF VEGF-A 12:107 CRYSTALLIZED IN TETRAGONAL TITLE 2 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 3 CHAIN: V, W; COMPND 4 SYNONYM: VEGF-A,VASCULAR PERMEABILITY FACTOR,VPF; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: VEGFA, VEGF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B(+) KEYWDS GROWTH FACTOR, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.-F.GAUCHER,S.BROUSSY,M.REILLE-SEROUSSI REVDAT 3 24-JAN-24 6ZFL 1 REMARK REVDAT 2 06-JUL-22 6ZFL 1 JRNL REVDAT 1 30-JUN-21 6ZFL 0 JRNL AUTH J.F.GAUCHER,M.REILLE-SEROUSSI,S.BROUSSY JRNL TITL STRUCTURAL AND ITC CHARACTERIZATION OF PEPTIDE-PROTEIN JRNL TITL 2 BINDING: THERMODYNAMIC CONSEQUENCES OF CYCLIZATION JRNL TITL 3 CONSTRAINTS, A CASE STUDY ON VASCULAR ENDOTHELIAL GROWTH JRNL TITL 4 FACTOR LIGANDS. JRNL REF CHEMISTRY 2022 JRNL REFN ISSN 0947-6539 JRNL PMID 35665969 JRNL DOI 10.1002/CHEM.202200465 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18_3855 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 41352 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2069 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.1700 - 3.9500 0.98 2716 136 0.1595 0.1684 REMARK 3 2 3.9400 - 3.1300 1.00 2632 147 0.1395 0.1697 REMARK 3 3 3.1300 - 2.7400 1.00 2652 145 0.1532 0.1640 REMARK 3 4 2.7400 - 2.4900 0.98 2591 141 0.1555 0.1756 REMARK 3 5 2.4900 - 2.3100 1.00 2632 143 0.1490 0.1922 REMARK 3 6 2.3100 - 2.1700 1.00 2626 129 0.1576 0.1742 REMARK 3 7 2.1700 - 2.0600 1.00 2628 132 0.1615 0.1692 REMARK 3 8 2.0600 - 1.9700 1.00 2641 124 0.1570 0.2018 REMARK 3 9 1.9700 - 1.9000 1.00 2603 132 0.1705 0.2060 REMARK 3 10 1.9000 - 1.8300 0.99 2555 158 0.1895 0.1927 REMARK 3 11 1.8300 - 1.7700 1.00 2587 153 0.2013 0.2464 REMARK 3 12 1.7700 - 1.7200 1.00 2642 126 0.2110 0.2692 REMARK 3 13 1.7200 - 1.6800 1.00 2572 155 0.2415 0.2358 REMARK 3 14 1.6800 - 1.6400 0.99 2623 113 0.2510 0.3023 REMARK 3 15 1.6400 - 1.6000 0.99 2583 135 0.2624 0.2867 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.157 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.303 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 1703 REMARK 3 ANGLE : 1.023 2319 REMARK 3 CHIRALITY : 0.061 242 REMARK 3 PLANARITY : 0.007 304 REMARK 3 DIHEDRAL : 18.118 681 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 12 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.4760 20.8032 -2.9943 REMARK 3 T TENSOR REMARK 3 T11: 0.1439 T22: 0.1521 REMARK 3 T33: 0.1227 T12: 0.0299 REMARK 3 T13: -0.0126 T23: -0.0181 REMARK 3 L TENSOR REMARK 3 L11: 7.2057 L22: 1.8548 REMARK 3 L33: 4.6289 L12: -0.2459 REMARK 3 L13: -5.3752 L23: -0.0706 REMARK 3 S TENSOR REMARK 3 S11: 0.0216 S12: -0.5125 S13: 0.0935 REMARK 3 S21: 0.2198 S22: 0.0565 S23: -0.0765 REMARK 3 S31: -0.3765 S32: 0.4536 S33: -0.1229 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 27 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.1109 30.6784 5.5453 REMARK 3 T TENSOR REMARK 3 T11: 0.1815 T22: 0.1668 REMARK 3 T33: 0.1180 T12: 0.0300 REMARK 3 T13: 0.0026 T23: -0.0311 REMARK 3 L TENSOR REMARK 3 L11: 5.3815 L22: 7.7594 REMARK 3 L33: 1.1135 L12: -6.4067 REMARK 3 L13: 1.8542 L23: -1.9567 REMARK 3 S TENSOR REMARK 3 S11: 0.2435 S12: -0.0563 S13: -0.2662 REMARK 3 S21: -0.1873 S22: -0.1108 S23: 0.3516 REMARK 3 S31: 0.1957 S32: -0.0082 S33: -0.1090 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 39 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2448 30.0437 6.9647 REMARK 3 T TENSOR REMARK 3 T11: 0.1885 T22: 0.2074 REMARK 3 T33: 0.1153 T12: 0.0245 REMARK 3 T13: 0.0207 T23: 0.0006 REMARK 3 L TENSOR REMARK 3 L11: 4.5465 L22: 2.9487 REMARK 3 L33: 1.5606 L12: -2.2733 REMARK 3 L13: 0.1870 L23: -0.2306 REMARK 3 S TENSOR REMARK 3 S11: -0.1287 S12: -0.2614 S13: -0.3009 REMARK 3 S21: -0.0163 S22: 0.1343 S23: 0.2750 REMARK 3 S31: 0.2092 S32: -0.1496 S33: 0.0013 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 66 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.3436 32.9565 12.3664 REMARK 3 T TENSOR REMARK 3 T11: 0.1432 T22: 0.1509 REMARK 3 T33: 0.1045 T12: 0.0133 REMARK 3 T13: 0.0049 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 4.4268 L22: 7.1694 REMARK 3 L33: 2.6122 L12: -5.1457 REMARK 3 L13: 0.3987 L23: -1.7712 REMARK 3 S TENSOR REMARK 3 S11: -0.1378 S12: -0.1649 S13: -0.1811 REMARK 3 S21: 0.1847 S22: 0.1177 S23: 0.2591 REMARK 3 S31: -0.0825 S32: 0.0376 S33: 0.0106 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 84 THROUGH 99 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.4776 41.3558 9.7711 REMARK 3 T TENSOR REMARK 3 T11: 0.2143 T22: 0.2115 REMARK 3 T33: 0.1813 T12: 0.0894 REMARK 3 T13: -0.0220 T23: -0.0515 REMARK 3 L TENSOR REMARK 3 L11: 4.5229 L22: 2.7761 REMARK 3 L33: 2.8710 L12: -1.3868 REMARK 3 L13: 1.5396 L23: -1.8153 REMARK 3 S TENSOR REMARK 3 S11: 0.1327 S12: 0.1321 S13: 0.1403 REMARK 3 S21: -0.1700 S22: -0.1360 S23: 0.5373 REMARK 3 S31: -0.2811 S32: -0.4099 S33: -0.0009 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 100 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.4587 19.1311 14.4684 REMARK 3 T TENSOR REMARK 3 T11: 0.3773 T22: 0.3773 REMARK 3 T33: 0.2277 T12: 0.0948 REMARK 3 T13: 0.0268 T23: 0.0798 REMARK 3 L TENSOR REMARK 3 L11: 3.3171 L22: 1.3094 REMARK 3 L33: 6.7634 L12: -0.3740 REMARK 3 L13: 0.0260 L23: 0.6563 REMARK 3 S TENSOR REMARK 3 S11: -0.2690 S12: -0.4953 S13: -0.4714 REMARK 3 S21: 0.7993 S22: 0.2835 S23: 0.0069 REMARK 3 S31: 0.7431 S32: 0.2598 S33: 0.0613 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 12 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.7608 43.8242 3.2383 REMARK 3 T TENSOR REMARK 3 T11: 0.2216 T22: 0.1402 REMARK 3 T33: 0.1383 T12: 0.0030 REMARK 3 T13: 0.0363 T23: -0.0022 REMARK 3 L TENSOR REMARK 3 L11: 1.4552 L22: 6.6012 REMARK 3 L33: 5.7885 L12: 0.2688 REMARK 3 L13: 0.7552 L23: 4.9824 REMARK 3 S TENSOR REMARK 3 S11: 0.0192 S12: 0.2550 S13: 0.0710 REMARK 3 S21: -0.4166 S22: 0.3200 S23: -0.1995 REMARK 3 S31: -0.6897 S32: 0.7499 S33: -0.2113 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 27 THROUGH 45 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.7611 16.6158 -7.2909 REMARK 3 T TENSOR REMARK 3 T11: 0.1751 T22: 0.2141 REMARK 3 T33: 0.2387 T12: -0.0292 REMARK 3 T13: 0.0122 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 3.4939 L22: 2.7944 REMARK 3 L33: 3.2276 L12: -2.7393 REMARK 3 L13: -0.0150 L23: -0.7961 REMARK 3 S TENSOR REMARK 3 S11: -0.1405 S12: -0.0533 S13: -0.6665 REMARK 3 S21: 0.0189 S22: 0.1897 S23: 0.5094 REMARK 3 S31: 0.2995 S32: -0.3574 S33: -0.0087 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 46 THROUGH 84 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.8300 23.5270 -8.4625 REMARK 3 T TENSOR REMARK 3 T11: 0.1685 T22: 0.1537 REMARK 3 T33: 0.1112 T12: 0.0279 REMARK 3 T13: 0.0268 T23: -0.0133 REMARK 3 L TENSOR REMARK 3 L11: 3.1053 L22: 4.3780 REMARK 3 L33: 1.3389 L12: -2.8879 REMARK 3 L13: 0.5717 L23: -0.0188 REMARK 3 S TENSOR REMARK 3 S11: -0.1011 S12: 0.0091 S13: -0.1723 REMARK 3 S21: 0.0906 S22: 0.0230 S23: 0.2818 REMARK 3 S31: -0.0364 S32: -0.2129 S33: 0.0632 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 85 THROUGH 99 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.8183 13.0547 -10.9507 REMARK 3 T TENSOR REMARK 3 T11: 0.1655 T22: 0.1356 REMARK 3 T33: 0.1529 T12: 0.0282 REMARK 3 T13: 0.0345 T23: -0.0135 REMARK 3 L TENSOR REMARK 3 L11: 1.1891 L22: 7.2430 REMARK 3 L33: 1.7231 L12: -1.9217 REMARK 3 L13: 0.6548 L23: -0.2707 REMARK 3 S TENSOR REMARK 3 S11: 0.1694 S12: 0.2141 S13: -0.2651 REMARK 3 S21: -0.2732 S22: -0.1747 S23: -0.0690 REMARK 3 S31: 0.2676 S32: -0.0009 S33: 0.0198 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 100 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.9189 35.7036 -14.0388 REMARK 3 T TENSOR REMARK 3 T11: 0.2852 T22: 0.3433 REMARK 3 T33: 0.1552 T12: 0.0891 REMARK 3 T13: -0.0159 T23: 0.0262 REMARK 3 L TENSOR REMARK 3 L11: 1.0535 L22: 5.7247 REMARK 3 L33: 3.8969 L12: -2.3466 REMARK 3 L13: 0.3664 L23: 0.5531 REMARK 3 S TENSOR REMARK 3 S11: 0.3012 S12: 0.7898 S13: 0.3397 REMARK 3 S21: -0.3884 S22: -0.2904 S23: 0.2760 REMARK 3 S31: -0.2992 S32: -0.5959 S33: 0.0714 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6ZFL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.272 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41413 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 44.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.69300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.18_3855 REMARK 200 STARTING MODEL: 1FLT REMARK 200 REMARK 200 REMARK: ELONGATED RODE 20 X 20 X 200UM REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (VEGF)2:2 PEPTIDE_2C COMPLEX PURIFIED REMARK 280 ON SEC AND CONCENTRATED AT 17MG/ML IN TRIS/HCL 10MM PH 8.5. (SEE REMARK 280 ID 6Z3F) MIX 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : TRIS/HCL REMARK 280 100MM PH 8.5 / MPD 42% (V/V) / (NH4)2PO4 200MM, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 20.24450 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 10.12225 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 30.36675 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 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: 4020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: V, W 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS V 26 113.26 -22.95 REMARK 500 ASP V 63 109.47 -162.80 REMARK 500 HIS V 86 -2.82 75.27 REMARK 500 GLN V 87 -163.24 -109.99 REMARK 500 CYS W 26 111.66 -21.35 REMARK 500 GLU W 42 43.07 -109.40 REMARK 500 ASP W 63 112.47 -163.13 REMARK 500 HIS W 86 -6.53 85.16 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 MPD V 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD V 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 V 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD W 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD W 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 W 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 W 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6ZCD RELATED DB: PDB REMARK 900 RELATED ID: 6Z3F RELATED DB: PDB REMARK 900 RELATED ID: 6Z13 RELATED DB: PDB REMARK 900 RELATED ID: 6ZBR RELATED DB: PDB DBREF 6ZFL V 13 107 UNP P15692 VEGFA_HUMAN 219 313 DBREF 6ZFL W 13 107 UNP P15692 VEGFA_HUMAN 219 313 SEQADV 6ZFL MET V 12 UNP P15692 INITIATING METHIONINE SEQADV 6ZFL MET W 12 UNP P15692 INITIATING METHIONINE SEQRES 1 V 96 MET GLU VAL VAL LYS PHE MET ASP VAL TYR GLN ARG SER SEQRES 2 V 96 TYR CYS HIS PRO ILE GLU THR LEU VAL ASP ILE PHE GLN SEQRES 3 V 96 GLU TYR PRO ASP GLU ILE GLU TYR ILE PHE LYS PRO SER SEQRES 4 V 96 CYS VAL PRO LEU MET ARG CYS GLY GLY CYS CYS ASN ASP SEQRES 5 V 96 GLU GLY LEU GLU CYS VAL PRO THR GLU GLU SER ASN ILE SEQRES 6 V 96 THR MET GLN ILE MET ARG ILE LYS PRO HIS GLN GLY GLN SEQRES 7 V 96 HIS ILE GLY GLU MET SER PHE LEU GLN HIS ASN LYS CYS SEQRES 8 V 96 GLU CYS ARG PRO LYS SEQRES 1 W 96 MET GLU VAL VAL LYS PHE MET ASP VAL TYR GLN ARG SER SEQRES 2 W 96 TYR CYS HIS PRO ILE GLU THR LEU VAL ASP ILE PHE GLN SEQRES 3 W 96 GLU TYR PRO ASP GLU ILE GLU TYR ILE PHE LYS PRO SER SEQRES 4 W 96 CYS VAL PRO LEU MET ARG CYS GLY GLY CYS CYS ASN ASP SEQRES 5 W 96 GLU GLY LEU GLU CYS VAL PRO THR GLU GLU SER ASN ILE SEQRES 6 W 96 THR MET GLN ILE MET ARG ILE LYS PRO HIS GLN GLY GLN SEQRES 7 W 96 HIS ILE GLY GLU MET SER PHE LEU GLN HIS ASN LYS CYS SEQRES 8 W 96 GLU CYS ARG PRO LYS HET MPD V 201 22 HET MPD V 202 22 HET PO4 V 203 5 HET MPD W 201 22 HET MPD W 202 22 HET PO4 W 203 5 HET PO4 W 204 5 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM PO4 PHOSPHATE ION FORMUL 3 MPD 4(C6 H14 O2) FORMUL 5 PO4 3(O4 P 3-) FORMUL 10 HOH *208(H2 O) HELIX 1 AA1 LYS V 16 TYR V 25 1 10 HELIX 2 AA2 ILE V 35 TYR V 39 1 5 HELIX 3 AA3 PRO V 40 ILE V 43 5 4 HELIX 4 AA4 LYS W 16 TYR W 25 1 10 HELIX 5 AA5 ILE W 35 TYR W 39 1 5 HELIX 6 AA6 PRO W 40 ILE W 43 5 4 SHEET 1 AA1 3 VAL V 14 VAL V 15 0 SHEET 2 AA1 3 LEU W 66 LYS W 84 1 O GLN W 79 N VAL V 15 SHEET 3 AA1 3 ILE W 46 LYS W 48 -1 N LYS W 48 O MET W 81 SHEET 1 AA2 3 VAL V 14 VAL V 15 0 SHEET 2 AA2 3 LEU W 66 LYS W 84 1 O GLN W 79 N VAL V 15 SHEET 3 AA2 3 GLY W 88 PRO W 106 -1 O HIS W 90 N ARG W 82 SHEET 1 AA3 2 HIS V 27 ASP V 34 0 SHEET 2 AA3 2 CYS V 51 GLY V 58 -1 O LEU V 54 N THR V 31 SHEET 1 AA4 3 ILE V 46 LYS V 48 0 SHEET 2 AA4 3 LEU V 66 ILE V 83 -1 O MET V 81 N LYS V 48 SHEET 3 AA4 3 GLN V 89 PRO V 106 -1 O HIS V 90 N ARG V 82 SHEET 1 AA5 3 ILE V 46 LYS V 48 0 SHEET 2 AA5 3 LEU V 66 ILE V 83 -1 O MET V 81 N LYS V 48 SHEET 3 AA5 3 VAL W 14 VAL W 15 1 O VAL W 15 N GLN V 79 SHEET 1 AA6 2 HIS W 27 ASP W 34 0 SHEET 2 AA6 2 CYS W 51 GLY W 58 -1 O LEU W 54 N THR W 31 SSBOND 1 CYS V 26 CYS V 68 1555 1555 2.09 SSBOND 2 CYS V 51 CYS W 60 1555 1555 2.18 SSBOND 3 CYS V 57 CYS V 102 1555 1555 2.04 SSBOND 4 CYS V 60 CYS W 51 1555 1555 2.17 SSBOND 5 CYS V 61 CYS V 104 1555 1555 2.09 SSBOND 6 CYS W 26 CYS W 68 1555 1555 2.08 SSBOND 7 CYS W 57 CYS W 102 1555 1555 2.03 SSBOND 8 CYS W 61 CYS W 104 1555 1555 2.08 CISPEP 1 LYS V 48 PRO V 49 0 -9.95 CISPEP 2 LYS W 48 PRO W 49 0 -8.84 SITE 1 AC1 6 GLU V 73 ASN V 75 HOH V 326 PRO W 70 SITE 2 AC1 6 THR W 71 GLU W 73 SITE 1 AC2 3 GLY V 58 GLY V 59 HOH V 324 SITE 1 AC3 5 MET V 12 LYS V 101 HOH V 312 LYS W 16 SITE 2 AC3 5 HOH W 313 SITE 1 AC4 4 HOH V 307 GLY W 58 GLY W 59 HOH W 328 SITE 1 AC5 5 PRO V 70 THR V 71 GLU W 73 ASN W 75 SITE 2 AC5 5 HOH W 316 SITE 1 AC6 4 LYS V 16 MET W 12 LYS W 101 HOH W 327 SITE 1 AC7 4 TYR W 45 ARG W 82 GLN W 87 HIS W 90 CRYST1 88.340 88.340 40.489 90.00 90.00 90.00 P 41 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 0.011320 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011320 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024698 0.00000