HEADER PEPTIDE BINDING PROTEIN 10-JUN-20 6ZCD TITLE VEGF-A 13:107 CRYSTALLIZED WITH 1C BICYCLIC PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DERIVED FROM V114 PEPTIDE; COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DERIVED FROM V114 PEPTIDE FROM GENENTECH INC.; CG OF COMPND 6 ASP 14 AND NZ OF LYS 10 COVALENTLY LINKED BY LACTAM BRIDGE; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 9 CHAIN: V, W; COMPND 10 SYNONYM: VEGF-A,VASCULAR PERMEABILITY FACTOR,VPF; COMPND 11 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_VARIANT: ROSETTA2; SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_VECTOR: 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 6ZCD 1 REMARK REVDAT 2 06-JUL-22 6ZCD 1 JRNL REVDAT 1 23-JUN-21 6ZCD 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 21946 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1127 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 45.1700 - 3.6000 1.00 2804 125 0.1680 0.1903 REMARK 3 2 3.6000 - 2.8600 0.99 2608 152 0.1806 0.2590 REMARK 3 3 2.8600 - 2.5000 1.00 2598 153 0.1985 0.2765 REMARK 3 4 2.5000 - 2.2700 0.99 2580 139 0.1897 0.2179 REMARK 3 5 2.2700 - 2.1100 1.00 2586 140 0.1949 0.2607 REMARK 3 6 2.1100 - 1.9800 1.00 2545 140 0.2096 0.2581 REMARK 3 7 1.9800 - 1.8800 0.99 2565 142 0.2507 0.2967 REMARK 3 8 1.8800 - 1.8000 0.99 2533 136 0.2934 0.3475 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) : 0.221 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.403 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.36 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 1781 REMARK 3 ANGLE : 1.142 2408 REMARK 3 CHIRALITY : 0.063 247 REMARK 3 PLANARITY : 0.007 313 REMARK 3 DIHEDRAL : 20.050 687 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 13 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.1680 6.9514 8.0520 REMARK 3 T TENSOR REMARK 3 T11: 0.3812 T22: 0.2771 REMARK 3 T33: 0.3010 T12: 0.0041 REMARK 3 T13: -0.0380 T23: -0.0299 REMARK 3 L TENSOR REMARK 3 L11: 5.3033 L22: 5.9004 REMARK 3 L33: 5.0485 L12: 0.6352 REMARK 3 L13: -5.1586 L23: -1.0682 REMARK 3 S TENSOR REMARK 3 S11: -0.1492 S12: 0.2878 S13: -0.0056 REMARK 3 S21: -0.2532 S22: -0.1800 S23: 0.6573 REMARK 3 S31: -0.2011 S32: -0.8089 S33: 0.3024 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 27 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.9983 22.0064 -6.9915 REMARK 3 T TENSOR REMARK 3 T11: 0.4466 T22: 0.2202 REMARK 3 T33: 0.2695 T12: -0.0222 REMARK 3 T13: -0.0240 T23: 0.0255 REMARK 3 L TENSOR REMARK 3 L11: 4.8636 L22: 5.1553 REMARK 3 L33: 5.0150 L12: 5.0083 REMARK 3 L13: -4.9110 L23: -5.0366 REMARK 3 S TENSOR REMARK 3 S11: 0.3034 S12: -0.3836 S13: -0.4104 REMARK 3 S21: 0.8610 S22: -0.4944 S23: -0.6844 REMARK 3 S31: -0.2349 S32: 0.1713 S33: 0.2847 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 39 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.4181 20.1518 -7.8576 REMARK 3 T TENSOR REMARK 3 T11: 0.3452 T22: 0.3164 REMARK 3 T33: 0.2654 T12: 0.0481 REMARK 3 T13: -0.0207 T23: 0.0295 REMARK 3 L TENSOR REMARK 3 L11: 1.0144 L22: 9.1909 REMARK 3 L33: 3.6570 L12: 1.3620 REMARK 3 L13: -0.9911 L23: -3.5799 REMARK 3 S TENSOR REMARK 3 S11: -0.0225 S12: -0.0538 S13: -0.1620 REMARK 3 S21: -0.0989 S22: -0.3886 S23: -0.9256 REMARK 3 S31: 0.3673 S32: 0.4540 S33: 0.4355 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 66 THROUGH 99 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.5093 26.8281 -15.0392 REMARK 3 T TENSOR REMARK 3 T11: 0.3452 T22: 0.2354 REMARK 3 T33: 0.1692 T12: 0.0270 REMARK 3 T13: 0.0092 T23: 0.0281 REMARK 3 L TENSOR REMARK 3 L11: 0.8872 L22: 8.0929 REMARK 3 L33: 3.5739 L12: 0.6325 REMARK 3 L13: -0.6153 L23: -3.1150 REMARK 3 S TENSOR REMARK 3 S11: 0.0931 S12: 0.0321 S13: 0.0014 REMARK 3 S21: -0.3816 S22: -0.2488 S23: -0.2397 REMARK 3 S31: 0.0057 S32: 0.2353 S33: 0.1677 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'V' AND (RESID 100 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.0200 4.6379 -9.5993 REMARK 3 T TENSOR REMARK 3 T11: 0.8337 T22: 0.3548 REMARK 3 T33: 0.3112 T12: 0.1015 REMARK 3 T13: 0.0086 T23: -0.0151 REMARK 3 L TENSOR REMARK 3 L11: 3.6694 L22: 4.1274 REMARK 3 L33: 4.5352 L12: -2.5800 REMARK 3 L13: -3.0623 L23: 0.0158 REMARK 3 S TENSOR REMARK 3 S11: 0.1515 S12: 0.1782 S13: -0.4195 REMARK 3 S21: -0.3150 S22: -0.2999 S23: -0.0141 REMARK 3 S31: 2.1657 S32: 0.5748 S33: -0.1063 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 13 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.8128 33.0527 -7.7964 REMARK 3 T TENSOR REMARK 3 T11: 0.3846 T22: 0.2568 REMARK 3 T33: 0.2699 T12: 0.0285 REMARK 3 T13: 0.0656 T23: -0.0481 REMARK 3 L TENSOR REMARK 3 L11: 8.4125 L22: 6.3722 REMARK 3 L33: 4.5352 L12: 1.7325 REMARK 3 L13: 5.7433 L23: 1.8837 REMARK 3 S TENSOR REMARK 3 S11: -0.1499 S12: -0.2696 S13: 0.1325 REMARK 3 S21: 0.3283 S22: -0.1163 S23: 0.5077 REMARK 3 S31: -0.4065 S32: -1.0438 S33: 0.3319 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 27 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.0198 16.1824 6.2432 REMARK 3 T TENSOR REMARK 3 T11: 0.4162 T22: 0.3198 REMARK 3 T33: 0.1938 T12: -0.0421 REMARK 3 T13: 0.0643 T23: -0.0465 REMARK 3 L TENSOR REMARK 3 L11: 7.5055 L22: 9.6858 REMARK 3 L33: 8.7630 L12: -5.7858 REMARK 3 L13: 5.3082 L23: -6.2496 REMARK 3 S TENSOR REMARK 3 S11: 0.1763 S12: 0.4736 S13: 0.0037 REMARK 3 S21: -0.2709 S22: -0.1768 S23: -0.0734 REMARK 3 S31: -0.0748 S32: 0.8723 S33: 0.0562 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 39 THROUGH 45 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.3396 6.1765 14.1757 REMARK 3 T TENSOR REMARK 3 T11: 0.7180 T22: 0.8818 REMARK 3 T33: 0.7311 T12: 0.1027 REMARK 3 T13: -0.0990 T23: -0.4644 REMARK 3 L TENSOR REMARK 3 L11: 8.7055 L22: 1.5736 REMARK 3 L33: 8.3145 L12: 1.3986 REMARK 3 L13: -5.4644 L23: -3.4453 REMARK 3 S TENSOR REMARK 3 S11: -0.7949 S12: 0.2840 S13: -0.7735 REMARK 3 S21: -0.7252 S22: -0.4371 S23: 0.6486 REMARK 3 S31: 0.8789 S32: -0.7019 S33: 0.5272 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 46 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.2805 19.7004 5.1379 REMARK 3 T TENSOR REMARK 3 T11: 0.3998 T22: 0.2960 REMARK 3 T33: 0.1874 T12: -0.0143 REMARK 3 T13: 0.0297 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 1.0300 L22: 3.1116 REMARK 3 L33: 4.6291 L12: -0.8880 REMARK 3 L13: 0.3824 L23: -3.5191 REMARK 3 S TENSOR REMARK 3 S11: 0.0754 S12: 0.0597 S13: 0.1772 REMARK 3 S21: -0.0866 S22: -0.1702 S23: -0.2702 REMARK 3 S31: -0.3797 S32: 0.3830 S33: 0.1222 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 66 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.8645 11.9356 13.8043 REMARK 3 T TENSOR REMARK 3 T11: 0.4151 T22: 0.3270 REMARK 3 T33: 0.1886 T12: 0.0532 REMARK 3 T13: -0.0438 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 2.3140 L22: 4.2424 REMARK 3 L33: 2.7783 L12: 1.6731 REMARK 3 L13: -0.6564 L23: 0.0273 REMARK 3 S TENSOR REMARK 3 S11: 0.0511 S12: -0.0557 S13: -0.2400 REMARK 3 S21: 0.3551 S22: 0.0043 S23: -0.2338 REMARK 3 S31: 0.2015 S32: 0.5061 S33: -0.0542 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'W' AND (RESID 89 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.6430 19.7431 13.1573 REMARK 3 T TENSOR REMARK 3 T11: 0.3908 T22: 0.2948 REMARK 3 T33: 0.1874 T12: -0.0164 REMARK 3 T13: 0.0167 T23: -0.0306 REMARK 3 L TENSOR REMARK 3 L11: 1.1648 L22: 4.2285 REMARK 3 L33: 4.6033 L12: 0.9499 REMARK 3 L13: -0.3463 L23: -3.9863 REMARK 3 S TENSOR REMARK 3 S11: 0.0761 S12: -0.0908 S13: 0.0853 REMARK 3 S21: 0.3054 S22: -0.0082 S23: 0.1770 REMARK 3 S31: -0.3705 S32: 0.3435 S33: -0.0110 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.4365 43.0018 1.0014 REMARK 3 T TENSOR REMARK 3 T11: 1.4406 T22: 0.5872 REMARK 3 T33: 0.6562 T12: -0.0077 REMARK 3 T13: 0.0842 T23: -0.0506 REMARK 3 L TENSOR REMARK 3 L11: 8.1121 L22: 7.2461 REMARK 3 L33: 9.3027 L12: -4.7116 REMARK 3 L13: 3.9986 L23: -3.3478 REMARK 3 S TENSOR REMARK 3 S11: -0.1631 S12: 0.4155 S13: 1.7320 REMARK 3 S21: -0.5764 S22: -0.5764 S23: -0.7147 REMARK 3 S31: -2.9608 S32: -0.1915 S33: 0.7848 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 9 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.4799 46.3041 -8.2186 REMARK 3 T TENSOR REMARK 3 T11: 1.7187 T22: 0.6273 REMARK 3 T33: 0.8228 T12: 0.0497 REMARK 3 T13: -0.3706 T23: 0.0885 REMARK 3 L TENSOR REMARK 3 L11: 3.7542 L22: 0.4421 REMARK 3 L33: 1.3435 L12: 1.2885 REMARK 3 L13: -2.2460 L23: -0.7709 REMARK 3 S TENSOR REMARK 3 S11: -0.2672 S12: 0.7010 S13: 2.1805 REMARK 3 S21: 0.3036 S22: 0.0791 S23: 0.5026 REMARK 3 S31: -3.1542 S32: 0.0028 S33: 0.2663 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 6ZCD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109272. 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 : 22094 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 53.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.90200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (VEGF)2:2 PEPTIDE_1C COMPLEX PURIFIED REMARK 280 ON SEC AND CONCENTRATED AT 13.5MG/ML IN TRIS/HCL 10MM PH 8.5. REMARK 280 MIX 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : NAOAC/HCL 100MM PH REMARK 280 4.5 / MPD 35% (V/V) / (NH4)2PO4 150MM, VAPOR DIFFUSION, HANGING REMARK 280 DROP, 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 26.82200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.60500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.84950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.60500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.82200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.84950 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: 4980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.0 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 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 14 OD2 REMARK 470 LEU P 15 CA C O CB CG CD1 CD2 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 26 116.50 -25.58 REMARK 500 CYS W 26 113.06 -17.50 REMARK 500 HIS W 86 29.66 48.95 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 REMARK 900 RELATED ID: 6ZBR RELATED DB: PDB DBREF 6ZCD P 1 15 PDB 6ZCD 6ZCD 1 15 DBREF 6ZCD V 13 107 UNP P15692 VEGFA_HUMAN 39 133 DBREF 6ZCD 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 ASP 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 16 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 *124(H2 O) HELIX 1 AA1 TRP P 9 ASP 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 GLN V 98 N SER V 74 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 2.04 SSBOND 2 CYS V 26 CYS V 68 1555 1555 2.05 SSBOND 3 CYS V 51 CYS W 60 1555 1555 2.12 SSBOND 4 CYS V 57 CYS V 102 1555 1555 2.02 SSBOND 5 CYS V 60 CYS W 51 1555 1555 2.14 SSBOND 6 CYS V 61 CYS V 104 1555 1555 2.04 SSBOND 7 CYS W 26 CYS W 68 1555 1555 2.05 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 1.34 LINK C NLE P 6 N TRP P 7 1555 1555 1.33 CISPEP 1 LYS V 48 PRO V 49 0 -6.96 CISPEP 2 LYS W 48 PRO W 49 0 -6.18 SITE 1 AC1 3 ASN V 75 GLN V 89 ILE V 91 SITE 1 AC2 5 PRO V 70 GLN V 79 ILE V 91 GLU V 93 SITE 2 AC2 5 HOH V 324 SITE 1 AC3 5 PRO V 53 MET V 55 ILE V 76 GLN V 98 SITE 2 AC3 5 ARG W 23 SITE 1 AC4 4 ASP V 41 PRO W 70 HOH W 319 HOH W 337 SITE 1 AC5 5 HIS V 86 GLU W 42 ARG W 82 LYS W 101 SITE 2 AC5 5 HOH W 342 SITE 1 AC6 2 ASN W 75 ILE W 91 CRYST1 53.644 55.699 77.210 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 0.018641 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017954 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012952 0.00000