PDB Short entry for 2X1X HEADER HORMONE/SIGNALING PROTEIN 08-JAN-10 2X1X TITLE CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH DOMAINS 2 AND 3 OF VEGFR2 TITLE 2 IN A TETRAGONAL CRYSTAL FORM CAVEAT 2X1X NAG R 404 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR C; COMPND 3 CHAIN: E; COMPND 4 FRAGMENT: VEGF HOMOLOGY DOMAIN, RESIDUES 112-215; COMPND 5 SYNONYM: VEGF-C, VASCULAR ENDOTHELIAL GROWTH FACTOR-RELATED PROTEIN, COMPND 6 VRP, FLT4 LIGAND, FLT4-L; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2; COMPND 11 CHAIN: R; COMPND 12 FRAGMENT: IG-LIKE DOMAINS 2 AND 3, RESIDUES 120-326; COMPND 13 SYNONYM: VEGF RECEPTOR 2, VEGFR-2, KINASE INSERT DOMAIN RECEPTOR, COMPND 14 PROTEIN-TYROSINE KINASE RECEPTOR FLK-1; COMPND 15 ENGINEERED: YES 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: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFASTBAC; 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: SF9; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PFASTBAC KEYWDS HORMONE-SIGNALING PROTEIN COMPLEX, ANGIOGENESIS, GLYCOPROTEIN, HOST- KEYWDS 2 VIRUS INTERACTION, RECEPTOR, LYMPHANGIOGENESIS, IMMUNOGLOBULIN KEYWDS 3 DOMAIN, DEVELOPMENTAL PROTEIN, MITOGEN EXPDTA X-RAY DIFFRACTION AUTHOR V.-M.LEPPANEN,A.E.PROTA,M.JELTSCH,A.ANISIMOV,N.KALKKINEN,T.STRANDIN, AUTHOR 2 H.LANKINEN,A.GOLDMAN,K.BALLMER-HOFER,K.ALITALO REVDAT 5 29-JUL-20 2X1X 1 COMPND REMARK HETNAM SSBOND REVDAT 5 2 1 LINK SITE ATOM REVDAT 4 12-JUL-17 2X1X 1 REVDAT 3 10-AUG-11 2X1X 1 COMPND KEYWDS AUTHOR JRNL REVDAT 3 2 1 REMARK HETSYN SITE MASTER REVDAT 3 3 1 VERSN REVDAT 2 16-FEB-10 2X1X 1 KEYWDS REVDAT 1 09-FEB-10 2X1X 0 JRNL AUTH V.-M.LEPPANEN,A.E.PROTA,M.JELTSCH,A.ANISIMOV,N.KALKKINEN, JRNL AUTH 2 T.STRANDIN,H.LANKINEN,A.GOLDMAN,K.BALLMER-HOFER,K.ALITALO JRNL TITL STRUCTURAL DETERMINANTS OF GROWTH FACTOR BINDING AND JRNL TITL 2 SPECIFICITY BY VEGF RECEPTOR 2. JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 2425 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 20145116 JRNL DOI 10.1073/PNAS.0914318107 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 7273 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.273 REMARK 3 R VALUE (WORKING SET) : 0.266 REMARK 3 FREE R VALUE : 0.334 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 809 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 524 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3070 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2327 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 149 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.33000 REMARK 3 B22 (A**2) : 1.33000 REMARK 3 B33 (A**2) : -2.66000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.627 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.490 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 27.174 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.872 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.811 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2532 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3443 ; 1.114 ; 2.020 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 300 ; 5.865 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;37.224 ;23.804 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 403 ;17.845 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;15.800 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 422 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1796 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1510 ; 0.807 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2448 ; 1.503 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1022 ; 1.593 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 995 ; 2.851 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. RESIDUES E112, R120-R121, R128-R129 AND R206-R207 ARE REMARK 3 DISORDERED. RESIDUES Y114 AND E117 IN CHAIN E AND RESIDUES R122, REMARK 3 S130, D131, K144, K266, Q268 AND H269 IN CHAIN R HAD POOR REMARK 3 SIDECHAIN DENSITY AND WERE MODELED AS ALANINES. REMARK 4 REMARK 4 2X1X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1290042338. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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 : SI(111) MONOCHROMATOR REMARK 200 OPTICS : MIRRORS 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 : 8092 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 37.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 17.30 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2X1W REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NA-ACETATE BUFFER, PH 4.4-4.8, REMARK 280 50 MM CSCL, 28-32 % (W/V) JEFFAMINE 600, PH 4.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 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 0.000000 -1.000000 0.000000 44.36650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.36650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 52.63650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.36650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.36650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.63650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.36650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.36650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 52.63650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.36650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.36650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.63650 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, R, A, B, C, D 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 -88.73300 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN E, CYS 137 TO ALA 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 ALA E 112 REMARK 465 HIS E 216 REMARK 465 HIS E 217 REMARK 465 HIS E 218 REMARK 465 HIS E 219 REMARK 465 HIS E 220 REMARK 465 HIS E 221 REMARK 465 ASP R 120 REMARK 465 TYR R 121 REMARK 465 SER R 128 REMARK 465 VAL R 129 REMARK 465 ASP R 206 REMARK 465 GLU R 207 REMARK 465 ASP R 327 REMARK 465 PRO R 328 REMARK 465 ILE R 329 REMARK 465 GLU R 330 REMARK 465 GLY R 331 REMARK 465 ARG R 332 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 TYR E 114 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU E 117 CG CD OE1 OE2 REMARK 470 LYS E 128 CG CD CE NZ REMARK 470 LEU E 215 CG CD1 CD2 REMARK 470 ARG R 122 CG CD NE CZ NH1 NH2 REMARK 470 SER R 130 OG REMARK 470 ASP R 131 CG OD1 OD2 REMARK 470 LYS R 144 CG CD CE NZ REMARK 470 LYS R 183 CG CD CE NZ REMARK 470 LYS R 266 CG CD CE NZ REMARK 470 GLN R 268 CG CD OE1 NE2 REMARK 470 HIS R 269 CG ND1 CD2 CE1 NE2 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 ND2 ASN R 143 O5 NAG R 404 2.01 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 VAL E 146 -89.97 -62.42 REMARK 500 GLN E 194 -159.78 -92.85 REMARK 500 LYS R 144 -20.25 80.55 REMARK 500 PRO R 149 74.08 -69.40 REMARK 500 CYS R 150 48.72 -92.83 REMARK 500 ASN R 156 49.22 -75.21 REMARK 500 ARG R 176 -63.77 171.32 REMARK 500 TYR R 221 -21.30 -145.78 REMARK 500 SER R 281 -63.10 59.30 REMARK 500 SER R 283 -116.27 -21.64 REMARK 500 GLU R 284 36.42 -150.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG A 1 REMARK 610 NAG B 1 REMARK 610 NAG C 1 REMARK 610 NAG D 1 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG R 401 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS R 162 SG REMARK 620 2 HOH R 505 O 84.2 REMARK 620 3 HOH R 508 O 119.3 156.5 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y6A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VEGFR2 IN COMPLEX WITH A 2-ANILINO-5-ARYL- REMARK 900 OXAZOLE INHIBITOR REMARK 900 RELATED ID: 1Y6B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VEGFR2 IN COMPLEX WITH A 2-ANILINO-5-ARYL- REMARK 900 OXAZOLE INHIBITOR REMARK 900 RELATED ID: 1YWN RELATED DB: PDB REMARK 900 VEGFR2 IN COMPLEX WITH A NOVEL 4-AMINO- FURO[2,3-D]PYRIMIDINE REMARK 900 RELATED ID: 1VR2 RELATED DB: PDB REMARK 900 HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 (KDR) KINASE REMARK 900 DOMAIN REMARK 900 RELATED ID: 2X1W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH DOMAINS 2 AND 3 OF REMARK 900 VEGFR2 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE VEGF-C PROTEIN STUDIED COVERS RESIDUES 112-215 WITH A C- REMARK 999 TERMINAL 6HIS-TAG AND A C137A MUTATION. REMARK 999 THE VEGFR-2 PROTEIN STUDIED COVERS RESIDUES 120-326 WITH THE REMARK 999 ARTIFICIAL RESIDUES DPIEGR AT THE C-TERMINUS. DBREF 2X1X E 112 215 UNP P49767 VEGFC_HUMAN 112 215 DBREF 2X1X E 216 221 PDB 2X1X 2X1X 216 221 DBREF 2X1X R 120 326 UNP P35968 VGFR2_HUMAN 120 326 DBREF 2X1X R 327 332 PDB 2X1X 2X1X 327 332 SEQADV 2X1X ALA E 137 UNP P49767 CYS 137 ENGINEERED MUTATION SEQRES 1 E 110 ALA HIS TYR ASN THR GLU ILE LEU LYS SER ILE ASP ASN SEQRES 2 E 110 GLU TRP ARG LYS THR GLN CYS MET PRO ARG GLU VAL ALA SEQRES 3 E 110 ILE ASP VAL GLY LYS GLU PHE GLY VAL ALA THR ASN THR SEQRES 4 E 110 PHE PHE LYS PRO PRO CYS VAL SER VAL TYR ARG CYS GLY SEQRES 5 E 110 GLY CYS CYS ASN SER GLU GLY LEU GLN CYS MET ASN THR SEQRES 6 E 110 SER THR SER TYR LEU SER LYS THR LEU PHE GLU ILE THR SEQRES 7 E 110 VAL PRO LEU SER GLN GLY PRO LYS PRO VAL THR ILE SER SEQRES 8 E 110 PHE ALA ASN HIS THR SER CYS ARG CYS MET SER LYS LEU SEQRES 9 E 110 HIS HIS HIS HIS HIS HIS SEQRES 1 R 213 ASP TYR ARG SER PRO PHE ILE ALA SER VAL SER ASP GLN SEQRES 2 R 213 HIS GLY VAL VAL TYR ILE THR GLU ASN LYS ASN LYS THR SEQRES 3 R 213 VAL VAL ILE PRO CYS LEU GLY SER ILE SER ASN LEU ASN SEQRES 4 R 213 VAL SER LEU CYS ALA ARG TYR PRO GLU LYS ARG PHE VAL SEQRES 5 R 213 PRO ASP GLY ASN ARG ILE SER TRP ASP SER LYS LYS GLY SEQRES 6 R 213 PHE THR ILE PRO SER TYR MET ILE SER TYR ALA GLY MET SEQRES 7 R 213 VAL PHE CYS GLU ALA LYS ILE ASN ASP GLU SER TYR GLN SEQRES 8 R 213 SER ILE MET TYR ILE VAL VAL VAL VAL GLY TYR ARG ILE SEQRES 9 R 213 TYR ASP VAL VAL LEU SER PRO SER HIS GLY ILE GLU LEU SEQRES 10 R 213 SER VAL GLY GLU LYS LEU VAL LEU ASN CYS THR ALA ARG SEQRES 11 R 213 THR GLU LEU ASN VAL GLY ILE ASP PHE ASN TRP GLU TYR SEQRES 12 R 213 PRO SER SER LYS HIS GLN HIS LYS LYS LEU VAL ASN ARG SEQRES 13 R 213 ASP LEU LYS THR GLN SER GLY SER GLU MET LYS LYS PHE SEQRES 14 R 213 LEU SER THR LEU THR ILE ASP GLY VAL THR ARG SER ASP SEQRES 15 R 213 GLN GLY LEU TYR THR CYS ALA ALA SER SER GLY LEU MET SEQRES 16 R 213 THR LYS LYS ASN SER THR PHE VAL ARG VAL HIS GLU ASP SEQRES 17 R 213 PRO ILE GLU GLY ARG MODRES 2X1X ASN R 143 ASN GLYCOSYLATION SITE HET NAG A 1 14 HET NAG A 2 14 HET BMA A 3 11 HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET HG R 401 1 HET NAG R 404 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM HG MERCURY (II) ION FORMUL 3 NAG 9(C8 H15 N O6) FORMUL 3 BMA 2(C6 H12 O6) FORMUL 7 HG HG 2+ FORMUL 9 HOH *12(H2 O) HELIX 1 AA1 HIS E 113 THR E 129 1 17 HELIX 2 AA2 VAL E 140 PHE E 144 1 5 HELIX 3 AA3 TYR R 190 ILE R 192 5 3 HELIX 4 AA4 THR R 298 GLN R 302 5 5 SHEET 1 AA1 2 MET E 132 ASP E 139 0 SHEET 2 AA1 2 CYS E 156 GLY E 163 -1 O ARG E 161 N ARG E 134 SHEET 1 AA2 3 THR E 150 LYS E 153 0 SHEET 2 AA2 3 LEU E 171 THR E 189 -1 O ILE E 188 N PHE E 151 SHEET 3 AA2 3 LYS E 197 SER E 213 -1 O ASN E 205 N SER E 179 SHEET 1 AA3 5 HIS R 133 ILE R 138 0 SHEET 2 AA3 5 MET R 213 VAL R 218 1 O VAL R 217 N VAL R 136 SHEET 3 AA3 5 MET R 197 ALA R 202 -1 N VAL R 198 O TYR R 214 SHEET 4 AA3 5 VAL R 159 ARG R 164 -1 N SER R 160 O GLU R 201 SHEET 5 AA3 5 LYS R 168 PHE R 170 -1 O LYS R 168 N ALA R 163 SHEET 1 AA4 4 HIS R 133 ILE R 138 0 SHEET 2 AA4 4 MET R 213 VAL R 218 1 O VAL R 217 N VAL R 136 SHEET 3 AA4 4 MET R 197 ALA R 202 -1 N VAL R 198 O TYR R 214 SHEET 4 AA4 4 TYR R 209 GLN R 210 -1 O TYR R 209 N ALA R 202 SHEET 1 AA5 3 THR R 145 ILE R 148 0 SHEET 2 AA5 3 GLY R 184 PRO R 188 -1 O ILE R 187 N VAL R 146 SHEET 3 AA5 3 SER R 178 ASP R 180 -1 N ASP R 180 O GLY R 184 SHEET 1 AA6 4 ILE R 223 SER R 229 0 SHEET 2 AA6 4 LEU R 242 THR R 250 -1 O ARG R 249 N TYR R 224 SHEET 3 AA6 4 LYS R 286 ILE R 294 -1 O SER R 290 N CYS R 246 SHEET 4 AA6 4 LYS R 270 LEU R 277 -1 N ARG R 275 O LEU R 289 SHEET 1 AA7 4 ILE R 234 SER R 237 0 SHEET 2 AA7 4 MET R 314 HIS R 325 1 O ARG R 323 N ILE R 234 SHEET 3 AA7 4 GLY R 303 SER R 311 -1 N GLY R 303 O VAL R 322 SHEET 4 AA7 4 ASP R 257 GLU R 261 -1 N GLU R 261 O THR R 306 SSBOND 1 CYS E 131 CYS E 173 1555 1555 2.04 SSBOND 2 CYS E 156 CYS E 165 1555 2455 2.29 SSBOND 3 CYS E 162 CYS E 209 1555 1555 2.04 SSBOND 4 CYS E 166 CYS E 211 1555 1555 2.04 SSBOND 5 CYS R 150 CYS R 200 1555 1555 2.02 SSBOND 6 CYS R 246 CYS R 307 1555 1555 2.03 LINK ND2 ASN R 143 C1 NAG R 404 1555 1555 1.27 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.44 LINK O4 NAG A 2 C1 BMA A 3 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK SG CYS R 162 HG HG R 401 1555 1555 2.39 LINK HG HG R 401 O HOH R 505 1555 1555 2.33 LINK HG HG R 401 O HOH R 508 1555 4445 2.58 CISPEP 1 LYS E 153 PRO E 154 0 0.67 CISPEP 2 VAL E 190 PRO E 191 0 -0.22 CISPEP 3 GLN E 194 GLY E 195 0 3.81 CISPEP 4 ASN R 141 LYS R 142 0 2.64 CISPEP 5 LYS R 142 ASN R 143 0 8.39 CISPEP 6 ARG R 164 TYR R 165 0 -4.97 CISPEP 7 TYR R 165 PRO R 166 0 0.08 CISPEP 8 GLY R 174 ASN R 175 0 6.43 CISPEP 9 SER R 229 PRO R 230 0 0.59 CISPEP 10 GLN R 280 SER R 281 0 -8.82 CRYST1 88.733 88.733 105.273 90.00 90.00 90.00 P 42 21 2 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 0.011270 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011270 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009499 0.00000