HEADER TRANSFERASE/HORMONE 10-JUN-13 4BSK TITLE CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH VEGFR-3 DOMAINS D1-2 CAVEAT 4BSK NAG A 301 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND-BINDING DOMAINS D1-2, RESIDUES 23-229; COMPND 5 SYNONYM: VEGFR-3, FMS-LIKE TYROSINE KINASE 4, FLT-4, TYROSINE-PROTEIN COMPND 6 KINASE RECEPTOR FLT4, VEGFR-3; COMPND 7 EC: 2.7.10.1; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: COVALENT N-GLYCOSYLATION IN ASN33, ASN104 AND ASN166; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR C; COMPND 12 CHAIN: C; COMPND 13 FRAGMENT: VEGF HOMOLOGY DOMAIN, RESIDUES 103-215; COMPND 14 SYNONYM: VEGF-C, FLT4 LIGAND, FLT4-L, VASCULAR ENDOTHELIAL GROWTH COMPND 15 FACTOR-RELATED PROTEIN, VRP, VEGF-C; COMPND 16 ENGINEERED: YES; COMPND 17 MUTATION: YES; COMPND 18 OTHER_DETAILS: COVALENT N-GLYCOSYLATION IN ASN175 AND ASN205 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFASTBAC1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 16 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: SF21; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PFASTBAC1 KEYWDS TRANSFERASE-HORMONE COMPLEX, TRANSFERASE, LYMPHANGIOGENESIS, KEYWDS 2 ANGIOGENESIS, IG DOMAIN, GLYCOPROTEIN, RECEPTOR TYROSINE KINASE, KEYWDS 3 DIMERIZATION EXPDTA X-RAY DIFFRACTION AUTHOR V.M.LEPPANEN,D.TVOROGOV,K.KISKO,A.E.PROTA,M.JELTSCH,A.ANISIMOV, AUTHOR 2 S.MARKOVIC-MUELLER,E.STUTTFELD,K.N.GOLDIE,K.BALLMER-HOFER,K.ALITALO REVDAT 8 20-DEC-23 4BSK 1 HETSYN REVDAT 7 29-JUL-20 4BSK 1 COMPND REMARK HETNAM SSBOND REVDAT 7 2 1 LINK SITE ATOM REVDAT 6 08-MAY-19 4BSK 1 REMARK REVDAT 5 24-APR-19 4BSK 1 SOURCE REVDAT 4 11-APR-18 4BSK 1 CAVEAT REMARK HELIX SHEET REVDAT 4 2 1 SSBOND LINK ATOM REVDAT 3 28-AUG-13 4BSK 1 REMARK REVDAT 2 21-AUG-13 4BSK 1 JRNL REVDAT 1 31-JUL-13 4BSK 0 JRNL AUTH V.-M.LEPPANEN,D.TVOROGOV,K.KISKO,A.E.PROTA,M.JELTSCH, JRNL AUTH 2 A.ANISIMOV,S.MARKOVIC-MUELLER,E.STUTTFELD,K.N.GOLDIE, JRNL AUTH 3 K.BALLMER-HOFER,K.ALITALO JRNL TITL STRUCTURAL AND MECHANISTIC INSIGHTS INTO VEGFR-3 LIGAND JRNL TITL 2 BINDING AND ACTIVATION JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 12960 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23878260 JRNL DOI 10.1073/PNAS.1301415110 REMARK 2 REMARK 2 RESOLUTION. 4.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 4.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 5721 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.338 REMARK 3 R VALUE (WORKING SET) : 0.334 REMARK 3 FREE R VALUE : 0.372 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 572 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 19.9199 - 6.6069 1.00 1319 146 0.2789 0.3239 REMARK 3 2 6.6069 - 5.2762 1.00 1280 143 0.4465 0.4526 REMARK 3 3 5.2762 - 4.6187 1.00 1275 141 0.4212 0.4770 REMARK 3 4 4.6187 - 4.2008 1.00 1275 142 0.3953 0.4379 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) : 0.960 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 52.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 135.9 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 : 0.004 1924 REMARK 3 ANGLE : 1.032 2651 REMARK 3 CHIRALITY : 0.061 337 REMARK 3 PLANARITY : 0.006 339 REMARK 3 DIHEDRAL : 15.257 615 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN C AND ((RESSEQ 115:213)) REMARK 3 ORIGIN FOR THE GROUP (A): -91.8644 0.2163 -14.9626 REMARK 3 T TENSOR REMARK 3 T11: 1.1568 T22: 0.9691 REMARK 3 T33: 0.8004 T12: -0.4292 REMARK 3 T13: -0.0070 T23: -0.2866 REMARK 3 L TENSOR REMARK 3 L11: 0.1414 L22: 0.5692 REMARK 3 L33: 0.1646 L12: -0.2792 REMARK 3 L13: 0.1414 L23: -0.2582 REMARK 3 S TENSOR REMARK 3 S11: 0.1784 S12: -0.1823 S13: -0.2764 REMARK 3 S21: 0.1889 S22: 0.2924 S23: 0.1795 REMARK 3 S31: 0.0955 S32: 0.1796 S33: 0.1417 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND ((RESSEQ 134:224)) REMARK 3 ORIGIN FOR THE GROUP (A): -72.0515 32.4435 -21.6582 REMARK 3 T TENSOR REMARK 3 T11: 0.7960 T22: 0.2624 REMARK 3 T33: 0.4524 T12: -0.8554 REMARK 3 T13: -0.3602 T23: -0.5938 REMARK 3 L TENSOR REMARK 3 L11: 0.0409 L22: 0.0466 REMARK 3 L33: 0.0149 L12: 0.0582 REMARK 3 L13: 0.0356 L23: 0.0425 REMARK 3 S TENSOR REMARK 3 S11: -0.0916 S12: -0.0886 S13: 0.0569 REMARK 3 S21: -0.0048 S22: -0.0077 S23: -0.1687 REMARK 3 S31: -0.1048 S32: 0.0191 S33: -0.1594 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND ((RESSEQ 28:133)) REMARK 3 ORIGIN FOR THE GROUP (A): -52.8065 53.2412 -18.6545 REMARK 3 T TENSOR REMARK 3 T11: 1.4476 T22: 0.7205 REMARK 3 T33: 1.3619 T12: -0.8562 REMARK 3 T13: 0.0124 T23: -0.1839 REMARK 3 L TENSOR REMARK 3 L11: 0.0452 L22: 0.0406 REMARK 3 L33: 0.0493 L12: 0.0392 REMARK 3 L13: -0.0501 L23: -0.0419 REMARK 3 S TENSOR REMARK 3 S11: 0.1695 S12: 0.1691 S13: 0.0979 REMARK 3 S21: 0.0215 S22: 0.3504 S23: -0.2343 REMARK 3 S31: -0.0848 S32: 0.0109 S33: 0.1428 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES 103-114 AND 213-215 IN VEGF-C REMARK 3 AND RESIDUES 23-27, 77-89, 114-123, 211-212 AND 225-229 IN VEGFR- REMARK 3 3 ARE DISORDERED. ATOMS OF DISORDERED SIDECHAINS WERE OMITTED REMARK 3 FROM THE FINAL MODEL. REMARK 4 REMARK 4 4BSK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1290057165. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA 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 : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5765 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.50 REMARK 200 R MERGE FOR SHELL (I) : 1.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: AUTOSHARP, MOLREP REMARK 200 STARTING MODEL: PDB ENTRIES 2X1X, 1FLT AND 2E9W REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SITTING DROPS AT ROOM TEMPERATURE OVER REMARK 280 A RESERVOIR SOLUTION OF 0.1 M BIS-TRIS BUFFER AT PH 8.5-9.5 AND REMARK 280 1.0-1.5 M AMMONIUM SULPHATE., PH 9, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+1/2 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 0.00000 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 0.00000 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 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 83.33000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 83.33000 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 83.33000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 83.33000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 83.33000 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 83.33000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 83.33000 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 83.33000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 83.33000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 83.33000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 83.33000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 83.33000 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 83.33000 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 83.33000 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 83.33000 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 83.33000 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 83.33000 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 83.33000 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 83.33000 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 83.33000 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 83.33000 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 83.33000 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 83.33000 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 83.33000 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 83.33000 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 83.33000 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 83.33000 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 83.33000 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 83.33000 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 83.33000 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 83.33000 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 83.33000 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 83.33000 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 83.33000 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 83.33000 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 83.33000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B 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 -166.66000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 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 SER A 23 REMARK 465 GLY A 24 REMARK 465 TYR A 25 REMARK 465 SER A 26 REMARK 465 MET A 27 REMARK 465 ASP A 77 REMARK 465 THR A 78 REMARK 465 GLY A 79 REMARK 465 VAL A 80 REMARK 465 VAL A 81 REMARK 465 ARG A 82 REMARK 465 ASP A 83 REMARK 465 CYS A 84 REMARK 465 GLU A 85 REMARK 465 GLY A 86 REMARK 465 THR A 87 REMARK 465 ASP A 88 REMARK 465 ALA A 89 REMARK 465 LYS A 114 REMARK 465 TYR A 115 REMARK 465 ILE A 116 REMARK 465 LYS A 117 REMARK 465 ALA A 118 REMARK 465 ARG A 119 REMARK 465 ILE A 120 REMARK 465 GLU A 121 REMARK 465 GLY A 122 REMARK 465 THR A 123 REMARK 465 GLY A 211 REMARK 465 ASP A 212 REMARK 465 THR A 225 REMARK 465 GLY A 226 REMARK 465 ASN A 227 REMARK 465 GLU A 228 REMARK 465 LEU A 229 REMARK 465 ALA A 230 REMARK 465 ASP A 231 REMARK 465 PRO A 232 REMARK 465 ILE A 233 REMARK 465 GLU A 234 REMARK 465 GLY A 235 REMARK 465 ARG A 236 REMARK 465 ASP C 101 REMARK 465 PRO C 102 REMARK 465 THR C 103 REMARK 465 GLU C 104 REMARK 465 GLU C 105 REMARK 465 THR C 106 REMARK 465 ILE C 107 REMARK 465 LYS C 108 REMARK 465 PHE C 109 REMARK 465 ALA C 110 REMARK 465 ALA C 111 REMARK 465 ALA C 112 REMARK 465 HIS C 113 REMARK 465 TYR C 114 REMARK 465 SER C 213 REMARK 465 LYS C 214 REMARK 465 LEU C 215 REMARK 465 HIS C 216 REMARK 465 HIS C 217 REMARK 465 HIS C 218 REMARK 465 HIS C 219 REMARK 465 HIS C 220 REMARK 465 HIS C 221 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 ILE A 34 CG1 CG2 CD1 REMARK 470 THR A 35 OG1 CG2 REMARK 470 ASP A 45 CG OD1 OD2 REMARK 470 SER A 46 OG REMARK 470 LEU A 47 CG CD1 CD2 REMARK 470 ARG A 52 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 TRP A 61 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 61 CZ3 CH2 REMARK 470 GLN A 65 CG CD OE1 NE2 REMARK 470 GLU A 66 CG CD OE1 OE2 REMARK 470 THR A 70 OG1 CG2 REMARK 470 LYS A 73 CG CD CE NZ REMARK 470 ASP A 74 CG OD1 OD2 REMARK 470 SER A 75 OG REMARK 470 GLU A 76 CG CD OE1 OE2 REMARK 470 ARG A 90 CG CD NE CZ NH1 NH2 REMARK 470 PRO A 91 CG CD REMARK 470 TYR A 92 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 CYS A 93 SG REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 LEU A 96 CG CD1 CD2 REMARK 470 LEU A 97 CG CD1 CD2 REMARK 470 LEU A 98 CG CD1 CD2 REMARK 470 HIS A 99 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 100 CG CD OE1 OE2 REMARK 470 HIS A 102 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 105 CG OD1 OD2 REMARK 470 TYR A 112 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR A 113 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 133 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 134 CG OD1 OD2 REMARK 470 PHE A 135 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 136 CG CD OE1 OE2 REMARK 470 GLN A 137 CG CD OE1 NE2 REMARK 470 LYS A 142 CG CD CE NZ REMARK 470 ASP A 144 CG OD1 OD2 REMARK 470 LEU A 146 CG CD1 CD2 REMARK 470 ASN A 149 CG OD1 ND2 REMARK 470 ARG A 150 CG CD NE CZ NH1 NH2 REMARK 470 MET A 154 CG SD CE REMARK 470 LEU A 159 CG CD1 CD2 REMARK 470 VAL A 160 CG1 CG2 REMARK 470 SER A 161 OG REMARK 470 ILE A 162 CG1 CG2 CD1 REMARK 470 LEU A 165 CG CD1 CD2 REMARK 470 ARG A 170 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 175 CG1 CG2 REMARK 470 LEU A 176 CG CD1 CD2 REMARK 470 ASP A 179 CG OD1 OD2 REMARK 470 GLN A 181 CG CD OE1 NE2 REMARK 470 GLU A 182 CG CD OE1 OE2 REMARK 470 ARG A 188 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 189 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 199 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 205 CG CD OE1 NE2 REMARK 470 GLU A 207 CG CD OE1 OE2 REMARK 470 TRP A 210 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 210 CZ3 CH2 REMARK 470 GLN A 213 CG CD OE1 NE2 REMARK 470 PHE A 215 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 218 CG OD1 ND2 REMARK 470 LEU A 221 CG CD1 CD2 REMARK 470 HIS A 223 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 224 CG1 CG2 CD1 REMARK 470 ASN C 115 CG OD1 ND2 REMARK 470 THR C 116 OG1 CG2 REMARK 470 GLU C 117 CG CD OE1 OE2 REMARK 470 ILE C 118 CG1 CG2 CD1 REMARK 470 LYS C 120 CG CD CE NZ REMARK 470 TRP C 126 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP C 126 CZ3 CH2 REMARK 470 ARG C 127 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 128 CG CD CE NZ REMARK 470 MET C 132 CG SD CE REMARK 470 ARG C 134 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 135 CG CD OE1 OE2 REMARK 470 LEU C 171 CG CD1 CD2 REMARK 470 GLN C 172 CG CD OE1 NE2 REMARK 470 MET C 174 CG SD CE REMARK 470 LEU C 181 CG CD1 CD2 REMARK 470 LEU C 185 CG CD1 CD2 REMARK 470 ILE C 188 CG1 CG2 CD1 REMARK 470 LEU C 192 CG CD1 CD2 REMARK 470 LYS C 197 CG CD CE NZ REMARK 470 MET C 212 CG SD CE 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 GLN A 54 -107.62 64.93 REMARK 500 PRO A 62 101.22 -57.48 REMARK 500 GLN A 65 -123.00 -138.64 REMARK 500 GLU A 66 19.39 56.54 REMARK 500 ASP A 74 -23.10 -147.60 REMARK 500 SER A 75 -74.27 64.70 REMARK 500 HIS A 102 -144.49 -121.59 REMARK 500 ASN A 104 26.47 -70.07 REMARK 500 LYS A 151 16.49 -154.71 REMARK 500 ASP A 152 -7.06 67.89 REMARK 500 SER A 171 -153.63 -157.75 REMARK 500 SER A 174 -163.84 55.57 REMARK 500 ARG A 189 -36.05 -155.64 REMARK 500 ASN A 218 82.88 -159.47 REMARK 500 PHE A 220 -155.53 -121.34 REMARK 500 THR C 116 -71.10 -56.20 REMARK 500 THR C 148 27.08 -76.37 REMARK 500 LEU C 192 60.37 -69.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BSJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VEGFR-3 EXTRACELLULAR DOMAINS D4-5 DBREF 4BSK A 23 229 UNP P35916 VGFR3_HUMAN 23 229 DBREF 4BSK C 103 215 UNP P49767 VEGFC_HUMAN 103 215 SEQADV 4BSK ALA A 230 UNP P35916 CLONING ARTIFACT SEQADV 4BSK ASP A 231 UNP P35916 CLONING ARTIFACT SEQADV 4BSK PRO A 232 UNP P35916 CLONING ARTIFACT SEQADV 4BSK ILE A 233 UNP P35916 CLONING ARTIFACT SEQADV 4BSK GLU A 234 UNP P35916 CLONING ARTIFACT SEQADV 4BSK GLY A 235 UNP P35916 CLONING ARTIFACT SEQADV 4BSK ARG A 236 UNP P35916 CLONING ARTIFACT SEQADV 4BSK ASP C 101 UNP P49767 EXPRESSION TAG SEQADV 4BSK PRO C 102 UNP P49767 EXPRESSION TAG SEQADV 4BSK ALA C 137 UNP P49767 CYS 137 ENGINEERED MUTATION SEQADV 4BSK HIS C 216 UNP P49767 EXPRESSION TAG SEQADV 4BSK HIS C 217 UNP P49767 EXPRESSION TAG SEQADV 4BSK HIS C 218 UNP P49767 EXPRESSION TAG SEQADV 4BSK HIS C 219 UNP P49767 EXPRESSION TAG SEQADV 4BSK HIS C 220 UNP P49767 EXPRESSION TAG SEQADV 4BSK HIS C 221 UNP P49767 EXPRESSION TAG SEQRES 1 A 214 SER GLY TYR SER MET THR PRO PRO THR LEU ASN ILE THR SEQRES 2 A 214 GLU GLU SER HIS VAL ILE ASP THR GLY ASP SER LEU SER SEQRES 3 A 214 ILE SER CYS ARG GLY GLN HIS PRO LEU GLU TRP ALA TRP SEQRES 4 A 214 PRO GLY ALA GLN GLU ALA PRO ALA THR GLY ASP LYS ASP SEQRES 5 A 214 SER GLU ASP THR GLY VAL VAL ARG ASP CYS GLU GLY THR SEQRES 6 A 214 ASP ALA ARG PRO TYR CYS LYS VAL LEU LEU LEU HIS GLU SEQRES 7 A 214 VAL HIS ALA ASN ASP THR GLY SER TYR VAL CYS TYR TYR SEQRES 8 A 214 LYS TYR ILE LYS ALA ARG ILE GLU GLY THR THR ALA ALA SEQRES 9 A 214 SER SER TYR VAL PHE VAL ARG ASP PHE GLU GLN PRO PHE SEQRES 10 A 214 ILE ASN LYS PRO ASP THR LEU LEU VAL ASN ARG LYS ASP SEQRES 11 A 214 ALA MET TRP VAL PRO CYS LEU VAL SER ILE PRO GLY LEU SEQRES 12 A 214 ASN VAL THR LEU ARG SER GLN SER SER VAL LEU TRP PRO SEQRES 13 A 214 ASP GLY GLN GLU VAL VAL TRP ASP ASP ARG ARG GLY MET SEQRES 14 A 214 LEU VAL SER THR PRO LEU LEU HIS ASP ALA LEU TYR LEU SEQRES 15 A 214 GLN CYS GLU THR THR TRP GLY ASP GLN ASP PHE LEU SER SEQRES 16 A 214 ASN PRO PHE LEU VAL HIS ILE THR GLY ASN GLU LEU ALA SEQRES 17 A 214 ASP PRO ILE GLU GLY ARG SEQRES 1 C 121 ASP PRO THR GLU GLU THR ILE LYS PHE ALA ALA ALA HIS SEQRES 2 C 121 TYR ASN THR GLU ILE LEU LYS SER ILE ASP ASN GLU TRP SEQRES 3 C 121 ARG LYS THR GLN CYS MET PRO ARG GLU VAL ALA ILE ASP SEQRES 4 C 121 VAL GLY LYS GLU PHE GLY VAL ALA THR ASN THR PHE PHE SEQRES 5 C 121 LYS PRO PRO CYS VAL SER VAL TYR ARG CYS GLY GLY CYS SEQRES 6 C 121 CYS ASN SER GLU GLY LEU GLN CYS MET ASN THR SER THR SEQRES 7 C 121 SER TYR LEU SER LYS THR LEU PHE GLU ILE THR VAL PRO SEQRES 8 C 121 LEU SER GLN GLY PRO LYS PRO VAL THR ILE SER PHE ALA SEQRES 9 C 121 ASN HIS THR SER CYS ARG CYS MET SER LYS LEU HIS HIS SEQRES 10 C 121 HIS HIS HIS HIS MODRES 4BSK ASN A 33 ASN GLYCOSYLATION SITE MODRES 4BSK ASN A 104 ASN GLYCOSYLATION SITE MODRES 4BSK ASN A 166 ASN GLYCOSYLATION SITE MODRES 4BSK ASN C 175 ASN GLYCOSYLATION SITE MODRES 4BSK ASN C 205 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG A 301 14 HET NAG A 302 14 HET NAG A 303 14 HET NAG C 303 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 NAG 6(C8 H15 N O6) HELIX 1 AA1 HIS A 102 THR A 106 5 5 HELIX 2 AA2 SER A 194 HIS A 199 1 6 HELIX 3 AA3 THR C 116 GLN C 130 1 15 HELIX 4 AA4 VAL C 140 GLY C 145 1 6 SHEET 1 AA1 4 SER A 38 ASP A 42 0 SHEET 2 AA1 4 SER A 127 ARG A 133 1 O ARG A 133 N ILE A 41 SHEET 3 AA1 4 GLY A 107 TYR A 112 -1 N GLY A 107 O VAL A 130 SHEET 4 AA1 4 GLU A 58 TRP A 59 -1 N GLU A 58 O TYR A 112 SHEET 1 AA2 3 LEU A 47 ARG A 52 0 SHEET 2 AA2 3 CYS A 93 LEU A 98 -1 O LEU A 96 N ILE A 49 SHEET 3 AA2 3 ALA A 69 THR A 70 -1 N THR A 70 O VAL A 95 SHEET 1 AA3 2 PHE A 139 ILE A 140 0 SHEET 2 AA3 2 LEU A 159 VAL A 160 -1 O LEU A 159 N ILE A 140 SHEET 1 AA4 3 MET A 154 TRP A 155 0 SHEET 2 AA4 3 GLY A 190 VAL A 193 -1 O VAL A 193 N MET A 154 SHEET 3 AA4 3 VAL A 184 ASP A 186 -1 N VAL A 184 O LEU A 192 SHEET 1 AA5 3 VAL A 175 LEU A 176 0 SHEET 2 AA5 3 THR A 168 ARG A 170 -1 N LEU A 169 O LEU A 176 SHEET 3 AA5 3 GLN A 205 GLU A 207 -1 O GLU A 207 N THR A 168 SHEET 1 AA6 2 MET C 132 ASP C 139 0 SHEET 2 AA6 2 CYS C 156 GLY C 163 -1 O VAL C 159 N VAL C 136 SHEET 1 AA7 3 PHE C 151 LYS C 153 0 SHEET 2 AA7 3 GLN C 172 ILE C 188 -1 O PHE C 186 N LYS C 153 SHEET 3 AA7 3 LYS C 197 MET C 212 -1 O SER C 208 N THR C 176 SSBOND 1 CYS A 51 CYS A 111 1555 1555 2.03 SSBOND 2 CYS A 158 CYS A 206 1555 1555 2.04 SSBOND 3 CYS C 131 CYS C 173 1555 1555 2.03 SSBOND 4 CYS C 156 CYS C 165 1555 2455 2.03 SSBOND 5 CYS C 162 CYS C 209 1555 1555 2.03 SSBOND 6 CYS C 166 CYS C 211 1555 1555 2.08 LINK ND2 ASN A 33 C1 NAG A 301 1555 1555 1.44 LINK ND2 ASN A 104 C1 NAG A 302 1555 1555 1.45 LINK ND2 ASN A 166 C1 NAG A 303 1555 1555 1.45 LINK ND2 ASN C 175 C1 NAG C 303 1555 1555 1.45 LINK ND2 ASN C 205 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 CISPEP 1 ALA A 64 GLN A 65 0 0.21 CISPEP 2 LYS A 142 PRO A 143 0 -11.37 CISPEP 3 LYS C 153 PRO C 154 0 -0.96 CISPEP 4 VAL C 190 PRO C 191 0 5.50 CRYST1 166.660 166.660 166.660 90.00 90.00 90.00 I 2 3 24 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 0.006000 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006000 0.00000