HEADER PEPTIDE BINDING PROTEIN 20-MAY-20 6Z3F TITLE VEGF-A 13:107 CRYSTALLIZED WITH 2C BICYCLIC PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAINS: P; COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 7 CHAIN: V, W; COMPND 8 SYNONYM: VEGF-A,VASCULAR PERMEABILITY FACTOR,VPF; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: DERIVED FROM V114 PEPTIDE - GENENTECH INC.; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: VEGFA, VEGF; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PET22B(+) KEYWDS GROWTH FACTOR, PEPTIDE LIGAND, LACTAM BRIDGE, ALPHA-HELIX KEYWDS 2 STABILIZATION, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.-F.GAUCHER,S.BROUSSY,M.REILLE-SEROUSSI REVDAT 3 01-MAY-24 6Z3F 1 REMARK REVDAT 2 06-JUL-22 6Z3F 1 JRNL REVDAT 1 02-JUN-21 6Z3F 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 14219 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 735 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 44.5500 - 3.5900 1.00 2864 132 0.1878 0.2124 REMARK 3 2 3.5900 - 2.8500 1.00 2709 153 0.2072 0.3197 REMARK 3 3 2.8500 - 2.4900 0.99 2642 158 0.2253 0.2636 REMARK 3 4 2.4900 - 2.2600 0.99 2640 142 0.2364 0.2909 REMARK 3 5 2.2600 - 2.1000 0.99 2629 150 0.2734 0.3308 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) : 0.208 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.122 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.55 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 : 0.002 1732 REMARK 3 ANGLE : 0.529 2331 REMARK 3 CHIRALITY : 0.044 239 REMARK 3 PLANARITY : 0.003 310 REMARK 3 DIHEDRAL : 18.563 663 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 13 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.5205 6.9916 8.1568 REMARK 3 T TENSOR REMARK 3 T11: 0.3682 T22: 0.2514 REMARK 3 T33: 0.3173 T12: -0.0088 REMARK 3 T13: -0.0353 T23: -0.0206 REMARK 3 L TENSOR REMARK 3 L11: 7.7799 L22: 5.8408 REMARK 3 L33: 4.0467 L12: 0.1386 REMARK 3 L13: -5.4561 L23: 0.9223 REMARK 3 S TENSOR REMARK 3 S11: -0.1252 S12: 0.0299 S13: 0.0958 REMARK 3 S21: -0.3088 S22: -0.5314 S23: 0.6665 REMARK 3 S31: -0.6907 S32: -0.7728 S33: 0.4528 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 27 THROUGH 89 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.7416 23.8103 -10.6674 REMARK 3 T TENSOR REMARK 3 T11: 0.3739 T22: 0.2791 REMARK 3 T33: 0.2950 T12: 0.0396 REMARK 3 T13: -0.0257 T23: 0.0062 REMARK 3 L TENSOR REMARK 3 L11: 0.7292 L22: 9.5631 REMARK 3 L33: 2.5158 L12: 0.5029 REMARK 3 L13: -0.6630 L23: -1.9347 REMARK 3 S TENSOR REMARK 3 S11: -0.0441 S12: -0.0404 S13: -0.0580 REMARK 3 S21: 0.0470 S22: -0.2059 S23: -0.8762 REMARK 3 S31: -0.0969 S32: 0.3283 S33: 0.2468 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 90 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.1540 17.2850 -13.3407 REMARK 3 T TENSOR REMARK 3 T11: 0.5741 T22: 0.2473 REMARK 3 T33: 0.2443 T12: 0.0189 REMARK 3 T13: 0.0110 T23: -0.0355 REMARK 3 L TENSOR REMARK 3 L11: 1.0557 L22: 8.5851 REMARK 3 L33: 1.9097 L12: 1.2668 REMARK 3 L13: -0.5544 L23: -0.6810 REMARK 3 S TENSOR REMARK 3 S11: -0.2063 S12: 0.0441 S13: -0.2610 REMARK 3 S21: -0.6811 S22: 0.3369 S23: -0.1819 REMARK 3 S31: 0.7725 S32: -0.1391 S33: 0.0177 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 13 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.1773 33.0160 -7.9287 REMARK 3 T TENSOR REMARK 3 T11: 0.3739 T22: 0.3824 REMARK 3 T33: 0.3563 T12: 0.0087 REMARK 3 T13: 0.0732 T23: -0.0498 REMARK 3 L TENSOR REMARK 3 L11: 4.1578 L22: 5.9471 REMARK 3 L33: 4.6951 L12: 0.0014 REMARK 3 L13: 4.1317 L23: 0.2087 REMARK 3 S TENSOR REMARK 3 S11: 0.1000 S12: -0.3733 S13: 0.4389 REMARK 3 S21: 0.4289 S22: -0.2900 S23: 0.7933 REMARK 3 S31: -0.5560 S32: -1.5279 S33: 0.0951 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 27 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.4787 16.3551 6.2840 REMARK 3 T TENSOR REMARK 3 T11: 0.3423 T22: 0.3472 REMARK 3 T33: 0.3208 T12: -0.0112 REMARK 3 T13: -0.0016 T23: -0.0620 REMARK 3 L TENSOR REMARK 3 L11: 7.7178 L22: 3.1740 REMARK 3 L33: 6.9899 L12: -4.8520 REMARK 3 L13: -0.2945 L23: 0.3142 REMARK 3 S TENSOR REMARK 3 S11: -0.5755 S12: -0.4431 S13: 0.1791 REMARK 3 S21: -0.3998 S22: 0.7678 S23: -0.5431 REMARK 3 S31: -0.1623 S32: 1.0957 S33: -0.2388 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 39 THROUGH 45 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.9176 6.2841 14.1906 REMARK 3 T TENSOR REMARK 3 T11: 0.7772 T22: 0.8395 REMARK 3 T33: 1.1158 T12: 0.0178 REMARK 3 T13: -0.1433 T23: -0.5454 REMARK 3 L TENSOR REMARK 3 L11: 5.1766 L22: 1.8536 REMARK 3 L33: 5.4986 L12: 2.4488 REMARK 3 L13: -4.2179 L23: -3.2078 REMARK 3 S TENSOR REMARK 3 S11: -0.8656 S12: 0.0186 S13: -1.2783 REMARK 3 S21: -1.6467 S22: -0.9652 S23: 0.7078 REMARK 3 S31: -0.6300 S32: -1.6336 S33: 1.2362 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 46 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.6955 19.7246 5.1733 REMARK 3 T TENSOR REMARK 3 T11: 0.5178 T22: 0.3753 REMARK 3 T33: 0.1861 T12: -0.0170 REMARK 3 T13: 0.0279 T23: -0.0279 REMARK 3 L TENSOR REMARK 3 L11: 1.7718 L22: 8.1221 REMARK 3 L33: 3.2527 L12: -0.5892 REMARK 3 L13: 0.3799 L23: -1.7262 REMARK 3 S TENSOR REMARK 3 S11: -0.0312 S12: 0.3072 S13: 0.1819 REMARK 3 S21: -0.1620 S22: 0.0581 S23: -0.2603 REMARK 3 S31: -0.5602 S32: 0.5616 S33: 0.0061 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 66 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.4307 17.8648 13.4493 REMARK 3 T TENSOR REMARK 3 T11: 0.5501 T22: 0.3359 REMARK 3 T33: 0.2109 T12: 0.0191 REMARK 3 T13: -0.0038 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 1.2235 L22: 4.9664 REMARK 3 L33: 2.9832 L12: 0.9162 REMARK 3 L13: -0.7304 L23: -0.6555 REMARK 3 S TENSOR REMARK 3 S11: -0.0235 S12: -0.0538 S13: -0.0114 REMARK 3 S21: 0.2261 S22: -0.0161 S23: -0.0302 REMARK 3 S31: 0.2945 S32: 0.4288 S33: 0.0282 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 84 THROUGH 89 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.9951 -7.4129 15.3283 REMARK 3 T TENSOR REMARK 3 T11: 1.0730 T22: 1.1499 REMARK 3 T33: 1.4142 T12: 0.4477 REMARK 3 T13: -0.2430 T23: 0.1026 REMARK 3 L TENSOR REMARK 3 L11: 2.4081 L22: 7.1310 REMARK 3 L33: 5.4149 L12: 1.5511 REMARK 3 L13: -0.3008 L23: -3.3299 REMARK 3 S TENSOR REMARK 3 S11: 0.2636 S12: 0.1727 S13: -1.2475 REMARK 3 S21: -0.4553 S22: -1.2306 S23: -2.2098 REMARK 3 S31: 1.6636 S32: 2.6742 S33: 1.1033 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 90 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.0984 21.3639 13.1319 REMARK 3 T TENSOR REMARK 3 T11: 0.6266 T22: 0.3660 REMARK 3 T33: 0.2360 T12: -0.0153 REMARK 3 T13: -0.0288 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.6167 L22: 7.3074 REMARK 3 L33: 4.4089 L12: 0.0329 REMARK 3 L13: -0.5038 L23: -3.4172 REMARK 3 S TENSOR REMARK 3 S11: 0.0332 S12: -0.0873 S13: 0.1887 REMARK 3 S21: 0.9291 S22: 0.1521 S23: -0.0022 REMARK 3 S31: -0.7314 S32: 0.4342 S33: -0.1410 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.9385 43.1010 0.9982 REMARK 3 T TENSOR REMARK 3 T11: 1.2050 T22: 0.5412 REMARK 3 T33: 0.6321 T12: 0.1048 REMARK 3 T13: 0.1106 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 7.2448 L22: 5.9513 REMARK 3 L33: 5.2443 L12: -0.9667 REMARK 3 L13: 0.5439 L23: -1.6406 REMARK 3 S TENSOR REMARK 3 S11: -0.5242 S12: -0.2006 S13: 1.2069 REMARK 3 S21: 0.6289 S22: 0.7630 S23: -0.3113 REMARK 3 S31: -1.6132 S32: -0.4275 S33: -0.1895 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 9 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.9009 46.3755 -8.6830 REMARK 3 T TENSOR REMARK 3 T11: 1.0428 T22: 0.4261 REMARK 3 T33: 0.5985 T12: -0.0134 REMARK 3 T13: -0.1470 T23: 0.1187 REMARK 3 L TENSOR REMARK 3 L11: 9.1356 L22: 8.2265 REMARK 3 L33: 3.4335 L12: 3.1592 REMARK 3 L13: -3.5692 L23: 0.7199 REMARK 3 S TENSOR REMARK 3 S11: 0.1841 S12: 0.6991 S13: 1.6315 REMARK 3 S21: -1.0914 S22: 0.6208 S23: 0.8123 REMARK 3 S31: -0.4696 S32: -0.1227 S33: -0.7817 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 6Z3F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292108820. 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) : 80 REMARK 200 PH : 4.5 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 1.18_3855 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14341 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 45.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.70100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: FLT1 REMARK 200 REMARK 200 REMARK: DIAMOND PLATE SHAPE 300 * 300UM REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (VEGF)2:2 PEPTIDE_3C COMPLEX PURIFIED REMARK 280 ON SEC AND CONCENTRATED AT 17MG/ML IN TRIS/HCL 10MM PH 8.5. MIX REMARK 280 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : NAOAC/HCL 100MM PH 4.5 / REMARK 280 MPD 35% (V/V) / (NH4)2PO4 150MM, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 27.20950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.79500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.91200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.79500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.20950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.91200 REMARK 290 SMTRY3 4 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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, 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 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 LEU P 15 REMARK 465 NH2 P 16 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP P 10 OD2 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 26 120.00 -28.31 REMARK 500 GLU V 30 107.67 -57.50 REMARK 500 ASP V 63 116.92 -170.41 REMARK 500 PRO V 106 153.34 -43.64 REMARK 500 CYS W 26 115.47 -26.48 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 NH2 P 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD V 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY V 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY V 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY V 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY W 201 DBREF 6Z3F P 1 16 PDB 6Z3F 6Z3F 1 16 DBREF 6Z3F V 13 107 UNP P15692 VEGFA_HUMAN 39 133 DBREF 6Z3F W 13 107 UNP P15692 VEGFA_HUMAN 39 133 SEQRES 1 P 16 CYS ASP ILE HIS VAL NLE TRP GLU TRP ASP CYS PHE GLU SEQRES 2 P 16 LYS LEU NH2 SEQRES 1 V 95 GLU VAL VAL LYS PHE MET ASP VAL TYR GLN ARG SER TYR SEQRES 2 V 95 CYS HIS PRO ILE GLU THR LEU VAL ASP ILE PHE GLN GLU SEQRES 3 V 95 TYR PRO ASP GLU ILE GLU TYR ILE PHE LYS PRO SER CYS SEQRES 4 V 95 VAL PRO LEU MET ARG CYS GLY GLY CYS CYS ASN ASP GLU SEQRES 5 V 95 GLY LEU GLU CYS VAL PRO THR GLU GLU SER ASN ILE THR SEQRES 6 V 95 MET GLN ILE MET ARG ILE LYS PRO HIS GLN GLY GLN HIS SEQRES 7 V 95 ILE GLY GLU MET SER PHE LEU GLN HIS ASN LYS CYS GLU SEQRES 8 V 95 CYS ARG PRO LYS SEQRES 1 W 95 GLU VAL VAL LYS PHE MET ASP VAL TYR GLN ARG SER TYR SEQRES 2 W 95 CYS HIS PRO ILE GLU THR LEU VAL ASP ILE PHE GLN GLU SEQRES 3 W 95 TYR PRO ASP GLU ILE GLU TYR ILE PHE LYS PRO SER CYS SEQRES 4 W 95 VAL PRO LEU MET ARG CYS GLY GLY CYS CYS ASN ASP GLU SEQRES 5 W 95 GLY LEU GLU CYS VAL PRO THR GLU GLU SER ASN ILE THR SEQRES 6 W 95 MET GLN ILE MET ARG ILE LYS PRO HIS GLN GLY GLN HIS SEQRES 7 W 95 ILE GLY GLU MET SER PHE LEU GLN HIS ASN LYS CYS GLU SEQRES 8 W 95 CYS ARG PRO LYS HET NLE P 6 16 HET NH2 P 101 1 HET MPD V 201 22 HET ACY V 202 7 HET ACY V 203 7 HET ACY V 204 7 HET ACY W 201 7 HET ACY W 202 7 HETNAM NLE NORLEUCINE HETNAM NH2 AMINO GROUP HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM ACY ACETIC ACID FORMUL 1 NLE C6 H13 N O2 FORMUL 4 NH2 H2 N FORMUL 5 MPD C6 H14 O2 FORMUL 6 ACY 5(C2 H4 O2) FORMUL 11 HOH *90(H2 O) HELIX 1 AA1 TRP P 9 LYS P 14 1 6 HELIX 2 AA2 LYS V 16 TYR V 25 1 10 HELIX 3 AA3 ILE V 35 TYR V 39 1 5 HELIX 4 AA4 PRO V 40 ILE V 43 5 4 HELIX 5 AA5 LYS W 16 TYR W 25 1 10 HELIX 6 AA6 ILE W 35 TYR W 39 1 5 HELIX 7 AA7 PRO W 40 ILE W 43 5 4 SHEET 1 AA1 2 HIS V 27 ASP V 34 0 SHEET 2 AA1 2 CYS V 51 GLY V 58 -1 O LEU V 54 N THR V 31 SHEET 1 AA2 3 ILE V 46 LYS V 48 0 SHEET 2 AA2 3 LEU V 66 ILE V 83 -1 O MET V 81 N LYS V 48 SHEET 3 AA2 3 HIS V 90 PRO V 106 -1 O HIS V 90 N ARG V 82 SHEET 1 AA3 3 ILE V 46 LYS V 48 0 SHEET 2 AA3 3 LEU V 66 ILE V 83 -1 O MET V 81 N LYS V 48 SHEET 3 AA3 3 VAL W 14 VAL W 15 1 O VAL W 15 N THR V 77 SHEET 1 AA4 2 HIS W 27 ASP W 34 0 SHEET 2 AA4 2 CYS W 51 GLY W 58 -1 O LEU W 54 N THR W 31 SHEET 1 AA5 3 ILE W 46 LYS W 48 0 SHEET 2 AA5 3 LEU W 66 ILE W 83 -1 O MET W 81 N LYS W 48 SHEET 3 AA5 3 GLN W 89 PRO W 106 -1 O GLN W 98 N SER W 74 SSBOND 1 CYS P 1 CYS P 11 1555 1555 2.03 SSBOND 2 CYS V 26 CYS V 68 1555 1555 2.03 SSBOND 3 CYS V 51 CYS W 60 1555 1555 2.04 SSBOND 4 CYS V 57 CYS V 102 1555 1555 2.03 SSBOND 5 CYS V 60 CYS W 51 1555 1555 2.04 SSBOND 6 CYS V 61 CYS V 104 1555 1555 2.03 SSBOND 7 CYS W 26 CYS W 68 1555 1555 2.03 SSBOND 8 CYS W 57 CYS W 102 1555 1555 2.03 SSBOND 9 CYS W 61 CYS W 104 1555 1555 2.03 LINK C VAL P 5 N NLE P 6 1555 1555 1.33 LINK C NLE P 6 N TRP P 7 1555 1555 1.33 LINK C LYS P 14 N NH2 P 101 1555 1555 1.33 CISPEP 1 LYS V 48 PRO V 49 0 -5.20 CISPEP 2 LYS W 48 PRO W 49 0 -3.64 SITE 1 AC1 1 LYS P 14 SITE 1 AC2 4 PHE P 12 GLU P 13 ASN V 75 GLN V 89 SITE 1 AC3 1 GLU W 42 SITE 1 AC4 3 GLU V 73 GLN V 79 GLU V 93 SITE 1 AC5 2 PRO V 53 GLN V 98 SITE 1 AC6 1 ASN W 75 CRYST1 54.419 55.824 77.590 90.00 90.00 90.00 P 21 21 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 0.018376 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017913 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012888 0.00000