HEADER PEPTIDE BINDING PROTEIN 09-JUN-20 6ZBR TITLE VEGF-A 13:107 CRYSTALLIZED WITH 4C BICYCLIC PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAINS: P; COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DERIVED FROM V114 PEPTIDE - GENENTECH INC.; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 8 CHAIN: V, W; COMPND 9 SYNONYM: VEGF-A,VASCULAR PERMEABILITY FACTOR,VPF; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 GENE: VEGFA, VEGF; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_CELL_LINE: ROSETTA2; SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PET22B(+) KEYWDS GROWTH FACTOR, PEPTIDE LIGAND, LACTAM BRIDGE, ALPHA-HELIX KEYWDS 2 STABILIZATION, SIGNALING PROTEIN, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.-F.GAUCHER,S.BROUSSY,M.REILLE-SEROUSSI REVDAT 3 24-JAN-24 6ZBR 1 REMARK REVDAT 2 06-JUL-22 6ZBR 1 JRNL REVDAT 1 23-JUN-21 6ZBR 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) : 45.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 31207 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1594 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 45.0900 - 3.5600 1.00 2906 132 0.1895 0.2083 REMARK 3 2 3.5600 - 2.8200 1.00 2728 155 0.1943 0.2515 REMARK 3 3 2.8200 - 2.4700 1.00 2701 159 0.2006 0.2541 REMARK 3 4 2.4700 - 2.2400 1.00 2698 148 0.1948 0.2336 REMARK 3 5 2.2400 - 2.0800 1.00 2658 156 0.1967 0.2196 REMARK 3 6 2.0800 - 1.9600 1.00 2685 141 0.1988 0.2363 REMARK 3 7 1.9600 - 1.8600 0.99 2657 131 0.2196 0.2431 REMARK 3 8 1.8600 - 1.7800 1.00 2675 142 0.2297 0.2718 REMARK 3 9 1.7800 - 1.7100 0.99 2641 141 0.2643 0.3231 REMARK 3 10 1.7100 - 1.6500 0.99 2627 146 0.2932 0.3386 REMARK 3 11 1.6500 - 1.6000 0.99 2637 143 0.3252 0.3467 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) : 0.192 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.022 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.79 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 1776 REMARK 3 ANGLE : 1.265 2403 REMARK 3 CHIRALITY : 0.062 247 REMARK 3 PLANARITY : 0.008 311 REMARK 3 DIHEDRAL : 20.485 690 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 15 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.9091 42.9338 1.1573 REMARK 3 T TENSOR REMARK 3 T11: 1.6898 T22: 0.4559 REMARK 3 T33: 0.6710 T12: -0.0815 REMARK 3 T13: 0.0308 T23: -0.0118 REMARK 3 L TENSOR REMARK 3 L11: 0.0566 L22: 0.0714 REMARK 3 L33: 0.0103 L12: 0.0764 REMARK 3 L13: -0.0298 L23: -0.0454 REMARK 3 S TENSOR REMARK 3 S11: 0.0435 S12: -0.0264 S13: 0.1976 REMARK 3 S21: 0.1591 S22: -0.0785 S23: -0.1320 REMARK 3 S31: -0.3320 S32: 0.1194 S33: -0.0408 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 9 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.0617 46.4722 -7.5790 REMARK 3 T TENSOR REMARK 3 T11: 1.8988 T22: -0.1516 REMARK 3 T33: 0.3850 T12: 0.3153 REMARK 3 T13: 0.0662 T23: -0.3321 REMARK 3 L TENSOR REMARK 3 L11: 0.2505 L22: 0.0153 REMARK 3 L33: 0.0296 L12: -0.0321 REMARK 3 L13: -0.0088 L23: 0.0192 REMARK 3 S TENSOR REMARK 3 S11: 0.1294 S12: 0.1216 S13: 0.2537 REMARK 3 S21: -0.1226 S22: -0.0976 S23: -0.0491 REMARK 3 S31: 0.0782 S32: -0.2014 S33: 0.0307 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 13 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.3946 6.9579 8.0763 REMARK 3 T TENSOR REMARK 3 T11: 0.2030 T22: 0.2677 REMARK 3 T33: 0.3367 T12: 0.0207 REMARK 3 T13: -0.0130 T23: -0.0297 REMARK 3 L TENSOR REMARK 3 L11: 0.1754 L22: 0.8649 REMARK 3 L33: 0.1198 L12: 0.1144 REMARK 3 L13: -0.0196 L23: -0.0706 REMARK 3 S TENSOR REMARK 3 S11: -0.0366 S12: 0.2247 S13: 0.1092 REMARK 3 S21: -0.3786 S22: -0.1717 S23: 0.4333 REMARK 3 S31: -0.4927 S32: -0.4195 S33: 0.0109 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 27 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.1856 21.9453 -6.9663 REMARK 3 T TENSOR REMARK 3 T11: 0.1646 T22: 0.2303 REMARK 3 T33: 0.3053 T12: -0.0269 REMARK 3 T13: -0.0487 T23: 0.0708 REMARK 3 L TENSOR REMARK 3 L11: 0.4801 L22: 1.2161 REMARK 3 L33: 0.8016 L12: 0.2755 REMARK 3 L13: 0.0633 L23: 0.8716 REMARK 3 S TENSOR REMARK 3 S11: 0.2130 S12: -0.3049 S13: -0.0900 REMARK 3 S21: 0.5998 S22: -0.5249 S23: -0.5591 REMARK 3 S31: -0.1039 S32: 0.2412 S33: -0.1497 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 39 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.9581 22.2827 -8.8203 REMARK 3 T TENSOR REMARK 3 T11: 0.1966 T22: 0.2883 REMARK 3 T33: 0.2963 T12: 0.0024 REMARK 3 T13: -0.0373 T23: 0.0371 REMARK 3 L TENSOR REMARK 3 L11: 0.3564 L22: 0.8303 REMARK 3 L33: 0.5901 L12: -0.6015 REMARK 3 L13: -0.1932 L23: 0.0667 REMARK 3 S TENSOR REMARK 3 S11: 0.0423 S12: -0.0026 S13: 0.0139 REMARK 3 S21: 0.1254 S22: -0.1526 S23: -0.4498 REMARK 3 S31: 0.1730 S32: 0.2612 S33: -0.0622 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 66 THROUGH 89 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.5316 26.8948 -14.3888 REMARK 3 T TENSOR REMARK 3 T11: 0.2361 T22: 0.2558 REMARK 3 T33: 0.2202 T12: -0.0025 REMARK 3 T13: 0.0144 T23: 0.0217 REMARK 3 L TENSOR REMARK 3 L11: 0.5179 L22: 0.3194 REMARK 3 L33: 0.8403 L12: -0.3538 REMARK 3 L13: 0.0584 L23: -0.4186 REMARK 3 S TENSOR REMARK 3 S11: 0.0958 S12: 0.0434 S13: 0.0920 REMARK 3 S21: -0.3071 S22: -0.2059 S23: -0.0415 REMARK 3 S31: 0.0470 S32: 0.2089 S33: 0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 90 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.9251 16.9335 -13.2344 REMARK 3 T TENSOR REMARK 3 T11: 0.2179 T22: 0.2123 REMARK 3 T33: 0.2255 T12: 0.0084 REMARK 3 T13: -0.0039 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: -0.0480 L22: 0.0407 REMARK 3 L33: 0.7467 L12: 0.0595 REMARK 3 L13: 0.1336 L23: -0.0056 REMARK 3 S TENSOR REMARK 3 S11: -0.0062 S12: 0.0532 S13: 0.0063 REMARK 3 S21: -0.0759 S22: 0.0866 S23: 0.1129 REMARK 3 S31: 0.2831 S32: -0.0613 S33: 0.0027 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 13 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.0969 32.9969 -7.8358 REMARK 3 T TENSOR REMARK 3 T11: 0.2710 T22: 0.2846 REMARK 3 T33: 0.3158 T12: 0.0122 REMARK 3 T13: 0.0168 T23: -0.0378 REMARK 3 L TENSOR REMARK 3 L11: 0.1268 L22: 1.1171 REMARK 3 L33: 0.5084 L12: 0.2601 REMARK 3 L13: -0.0942 L23: -0.6293 REMARK 3 S TENSOR REMARK 3 S11: 0.0054 S12: -0.1969 S13: 0.1386 REMARK 3 S21: 0.5768 S22: -0.1657 S23: 0.5269 REMARK 3 S31: -0.0743 S32: -0.7534 S33: 0.0223 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 27 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.2282 16.3915 6.2578 REMARK 3 T TENSOR REMARK 3 T11: 0.1918 T22: 0.3661 REMARK 3 T33: 0.2159 T12: 0.0098 REMARK 3 T13: -0.0184 T23: -0.0664 REMARK 3 L TENSOR REMARK 3 L11: 0.3279 L22: 0.7968 REMARK 3 L33: 1.6938 L12: -0.2962 REMARK 3 L13: -0.2155 L23: 1.1126 REMARK 3 S TENSOR REMARK 3 S11: -0.0494 S12: 0.1537 S13: 0.1462 REMARK 3 S21: -0.2150 S22: 0.3935 S23: -0.1703 REMARK 3 S31: -0.5790 S32: 0.8035 S33: 0.1779 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 39 THROUGH 45 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.7031 6.3603 13.9522 REMARK 3 T TENSOR REMARK 3 T11: 0.4070 T22: 0.7479 REMARK 3 T33: 0.7346 T12: 0.0683 REMARK 3 T13: -0.0482 T23: -0.2863 REMARK 3 L TENSOR REMARK 3 L11: 0.2031 L22: 0.5814 REMARK 3 L33: 0.3491 L12: 0.2351 REMARK 3 L13: -0.2554 L23: -0.4011 REMARK 3 S TENSOR REMARK 3 S11: -0.2455 S12: -0.1202 S13: -0.6362 REMARK 3 S21: -0.0234 S22: -0.4620 S23: -0.1948 REMARK 3 S31: -0.2620 S32: -0.2908 S33: -0.0325 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 46 THROUGH 58 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.7769 11.9487 7.9719 REMARK 3 T TENSOR REMARK 3 T11: 0.2647 T22: 0.2726 REMARK 3 T33: 0.1921 T12: 0.0127 REMARK 3 T13: -0.0020 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 0.1402 L22: 0.0610 REMARK 3 L33: 0.3971 L12: 0.0811 REMARK 3 L13: 0.1572 L23: 0.1481 REMARK 3 S TENSOR REMARK 3 S11: -0.1222 S12: 0.0850 S13: 0.0462 REMARK 3 S21: -0.2979 S22: 0.1771 S23: 0.0594 REMARK 3 S31: -0.1617 S32: 0.1618 S33: 0.0000 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 59 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.2527 35.5754 -0.8284 REMARK 3 T TENSOR REMARK 3 T11: 0.5376 T22: 0.3814 REMARK 3 T33: 0.2643 T12: -0.1175 REMARK 3 T13: -0.0100 T23: 0.0450 REMARK 3 L TENSOR REMARK 3 L11: 0.0195 L22: 0.0118 REMARK 3 L33: -0.0031 L12: 0.0030 REMARK 3 L13: -0.0066 L23: -0.0029 REMARK 3 S TENSOR REMARK 3 S11: 0.1018 S12: 0.3472 S13: 0.0869 REMARK 3 S21: 0.0292 S22: -0.0285 S23: 0.1486 REMARK 3 S31: -0.4534 S32: -0.2269 S33: 0.0000 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 66 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.1017 17.2302 13.4073 REMARK 3 T TENSOR REMARK 3 T11: 0.3198 T22: 0.2349 REMARK 3 T33: 0.2262 T12: -0.0014 REMARK 3 T13: 0.0131 T23: -0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.2548 L22: 0.1372 REMARK 3 L33: 0.6527 L12: 0.1691 REMARK 3 L13: -0.0339 L23: 0.1564 REMARK 3 S TENSOR REMARK 3 S11: -0.0079 S12: -0.0636 S13: 0.0034 REMARK 3 S21: 0.0569 S22: 0.0313 S23: 0.0449 REMARK 3 S31: 0.0160 S32: 0.2785 S33: 0.0000 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 84 THROUGH 89 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.4238 -7.7333 14.7999 REMARK 3 T TENSOR REMARK 3 T11: 0.5082 T22: 0.5868 REMARK 3 T33: 0.5703 T12: 0.0436 REMARK 3 T13: -0.1943 T23: 0.1221 REMARK 3 L TENSOR REMARK 3 L11: 0.0058 L22: -0.0017 REMARK 3 L33: 0.0147 L12: -0.0043 REMARK 3 L13: -0.0150 L23: 0.0120 REMARK 3 S TENSOR REMARK 3 S11: -0.2231 S12: 0.2120 S13: 0.0956 REMARK 3 S21: 0.0069 S22: -0.7599 S23: 0.0990 REMARK 3 S31: -0.2460 S32: -0.3205 S33: 0.0000 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 90 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.9084 21.2745 13.0087 REMARK 3 T TENSOR REMARK 3 T11: 0.3627 T22: 0.2458 REMARK 3 T33: 0.2151 T12: -0.0221 REMARK 3 T13: 0.0121 T23: -0.0024 REMARK 3 L TENSOR REMARK 3 L11: 0.1290 L22: 1.0595 REMARK 3 L33: 0.4942 L12: -0.0619 REMARK 3 L13: 0.0026 L23: -0.0830 REMARK 3 S TENSOR REMARK 3 S11: -0.0417 S12: -0.0726 S13: -0.0131 REMARK 3 S21: 0.0305 S22: 0.0957 S23: 0.1765 REMARK 3 S31: -0.2979 S32: 0.1918 S33: 0.0402 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 6ZBR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109162. 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 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31383 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 55.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.68200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: DIAMOND SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (VEGF)2:2 PEPTIDE_4C 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 27.03750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.53650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.80150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.53650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.03750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.80150 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: 4990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 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 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 GLU P 14 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH W 306 O HOH W 362 2.18 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 CYS V 26 114.32 -18.45 REMARK 500 CYS W 26 114.37 -12.76 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 MPD 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6Z3F RELATED DB: PDB REMARK 900 RELATED ID: 6Z13 RELATED DB: PDB DBREF 6ZBR P 1 15 PDB 6ZBR 6ZBR 1 15 DBREF 6ZBR V 13 107 UNP P15692 VEGFA_HUMAN 39 133 DBREF 6ZBR W 13 107 UNP P15692 VEGFA_HUMAN 39 133 SEQRES 1 P 15 CYS ASP ILE HIS VAL NLE TRP GLU TRP LYS CYS PHE GLU SEQRES 2 P 15 GLU LEU 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 19 HET MPD V 201 22 HET MPD V 202 22 HET MPD V 203 22 HET MPD W 201 22 HET MPD W 202 22 HET PO4 W 203 5 HETNAM NLE NORLEUCINE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM PO4 PHOSPHATE ION FORMUL 1 NLE C6 H13 N O2 FORMUL 4 MPD 5(C6 H14 O2) FORMUL 9 PO4 O4 P 3- FORMUL 10 HOH *145(H2 O) HELIX 1 AA1 GLU P 8 GLU P 14 1 7 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 PHE V 96 N ILE V 76 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 HIS W 90 PRO W 106 -1 O GLN W 98 N SER W 74 SSBOND 1 CYS P 1 CYS P 11 1555 1555 2.06 SSBOND 2 CYS V 26 CYS V 68 1555 1555 2.04 SSBOND 3 CYS V 51 CYS W 60 1555 1555 2.11 SSBOND 4 CYS V 57 CYS V 102 1555 1555 2.02 SSBOND 5 CYS V 60 CYS W 51 1555 1555 2.13 SSBOND 6 CYS V 61 CYS V 104 1555 1555 2.03 SSBOND 7 CYS W 26 CYS W 68 1555 1555 2.02 SSBOND 8 CYS W 57 CYS W 102 1555 1555 2.03 SSBOND 9 CYS W 61 CYS W 104 1555 1555 2.04 LINK C VAL P 5 N NLE P 6 1555 1555 1.34 LINK C NLE P 6 N TRP P 7 1555 1555 1.33 CISPEP 1 LYS V 48 PRO V 49 0 -9.75 CISPEP 2 LYS W 48 PRO W 49 0 -6.35 SITE 1 AC1 4 SER V 74 ASN V 75 MET V 81 LEU V 97 SITE 1 AC2 6 PRO V 70 THR V 71 GLN V 79 ILE V 91 SITE 2 AC2 6 GLU V 93 HOH V 309 SITE 1 AC3 3 PRO V 53 GLN V 98 ARG W 23 SITE 1 AC4 4 ASP V 41 GLN W 79 HOH W 331 HOH W 348 SITE 1 AC5 4 HIS V 86 GLU W 42 ARG W 82 LYS W 101 SITE 1 AC6 2 ASN W 75 GLN W 89 CRYST1 54.075 55.603 77.073 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 0.018493 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017985 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012975 0.00000