HEADER TRANSFERASE 25-AUG-11 3VHK TITLE CRYSTAL STRUCTURE OF THE VEGFR2 KINASE DOMAIN IN COMPLEX WITH A BACK TITLE 2 POCKET BINDER COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 806-1171; COMPND 5 SYNONYM: VEGFR-2, FETAL LIVER KINASE 1, FLK-1, KINASE INSERT DOMAIN COMPND 6 RECEPTOR, PROTEIN-TYROSINE KINASE RECEPTOR FLK-1; COMPND 7 EC: 2.7.10.1; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDR, FLK1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PFASTBAC KEYWDS VEGFR2, KINASE DOMAIN, COMPLEX, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.IWATA,H.OKI,K.OKADA,T.TAKAGI,M.TAWADA,Y.MIYAZAKI,S.IMAMURA,A.HORI, AUTHOR 2 M.S.HIXON,H.KIMURA,H.MIKI REVDAT 3 20-MAR-24 3VHK 1 REMARK SEQADV REVDAT 2 22-APR-15 3VHK 1 JRNL REVDAT 1 05-SEP-12 3VHK 0 JRNL AUTH H.IWATA,H.OKI,K.OKADA,T.TAKAGI,M.TAWADA,Y.MIYAZAKI, JRNL AUTH 2 S.IMAMURA,A.HORI,J.D.LAWSON,M.S.HIXON,H.KIMURA,H.MIKI JRNL TITL A BACK-TO-FRONT FRAGMENT-BASED DRUG DESIGN SEARCH STRATEGY JRNL TITL 2 TARGETING THE DFG-OUT POCKET OF PROTEIN TYROSINE KINASES. JRNL REF ACS MED.CHEM.LETT. V. 3 342 2012 JRNL REFN ISSN 1948-5875 JRNL PMID 24900475 JRNL DOI 10.1021/ML3000403 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REFMAC_5.2.0019 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) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 13619 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 681 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) : 2.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 894 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 38 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2395 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 42 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.27000 REMARK 3 B22 (A**2) : -2.14000 REMARK 3 B33 (A**2) : 0.74000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.70000 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): 0.291 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.230 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.393 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2480 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3344 ; 0.923 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 294 ; 4.922 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;32.821 ;22.768 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 437 ;13.891 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;14.122 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 357 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1902 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1015 ; 0.166 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1680 ; 0.298 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 53 ; 0.093 ; 0.200 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): 31 ; 0.136 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.156 ; 0.200 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): 1531 ; 1.900 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2381 ; 3.123 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1091 ; 4.759 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 963 ; 6.677 ; 6.000 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 814 A 920 REMARK 3 ORIGIN FOR THE GROUP (A): -33.6250 26.6600 8.6100 REMARK 3 T TENSOR REMARK 3 T11: 0.0912 T22: 0.0310 REMARK 3 T33: 0.0992 T12: 0.0361 REMARK 3 T13: 0.0199 T23: 0.0148 REMARK 3 L TENSOR REMARK 3 L11: 1.4794 L22: 2.9407 REMARK 3 L33: 2.9216 L12: 0.6539 REMARK 3 L13: 0.8126 L23: 0.8933 REMARK 3 S TENSOR REMARK 3 S11: -0.0916 S12: -0.0554 S13: 0.1007 REMARK 3 S21: -0.1424 S22: 0.1264 S23: 0.2141 REMARK 3 S31: 0.1530 S32: 0.1321 S33: -0.0349 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 921 A 1107 REMARK 3 RESIDUE RANGE : A 1124 A 1168 REMARK 3 ORIGIN FOR THE GROUP (A): -19.1130 29.4580 28.4870 REMARK 3 T TENSOR REMARK 3 T11: 0.1246 T22: 0.0590 REMARK 3 T33: 0.0635 T12: 0.0291 REMARK 3 T13: 0.0165 T23: 0.0099 REMARK 3 L TENSOR REMARK 3 L11: 2.6208 L22: 2.2453 REMARK 3 L33: 1.4570 L12: 0.2994 REMARK 3 L13: 0.9663 L23: 0.3779 REMARK 3 S TENSOR REMARK 3 S11: 0.0635 S12: -0.1440 S13: 0.0124 REMARK 3 S21: 0.2657 S22: -0.0364 S23: -0.0445 REMARK 3 S31: 0.2883 S32: 0.0986 S33: -0.0271 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1108 A 1123 REMARK 3 ORIGIN FOR THE GROUP (A): -11.5150 12.5320 36.6930 REMARK 3 T TENSOR REMARK 3 T11: 0.3758 T22: -0.0216 REMARK 3 T33: 0.3126 T12: 0.1301 REMARK 3 T13: -0.1784 T23: 0.3006 REMARK 3 L TENSOR REMARK 3 L11: 15.4673 L22: 5.3316 REMARK 3 L33: 7.1631 L12: -5.9839 REMARK 3 L13: -4.5837 L23: 5.9578 REMARK 3 S TENSOR REMARK 3 S11: 0.4148 S12: -0.7293 S13: -1.5921 REMARK 3 S21: 0.7015 S22: -0.3633 S23: -0.2303 REMARK 3 S31: 0.2881 S32: 0.3160 S33: -0.0515 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3VHK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000095052. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK 8.0SSI, CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : D*TREK 8.0SSI, CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13639 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 67.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.730 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.68 REMARK 200 R MERGE FOR SHELL (I) : 0.37700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES, 880-1440MM TRI-SODIUM REMARK 280 CITRATE, PH 7.0-8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 67.85950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.17700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.85950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.17700 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 GLY A 804 REMARK 465 ALA A 805 REMARK 465 MET A 806 REMARK 465 ASP A 807 REMARK 465 PRO A 808 REMARK 465 ASP A 809 REMARK 465 GLU A 810 REMARK 465 LEU A 811 REMARK 465 PRO A 812 REMARK 465 LEU A 813 REMARK 465 THR A 940 REMARK 465 LYS A 941 REMARK 465 GLY A 942 REMARK 465 ALA A 943 REMARK 465 ARG A 944 REMARK 465 PHE A 945 REMARK 465 ARG A 946 REMARK 465 GLN A 947 REMARK 465 GLY A 948 REMARK 465 LYS A 949 REMARK 465 ASP A 950 REMARK 465 TYR A 951 REMARK 465 VAL A 952 REMARK 465 GLY A 953 REMARK 465 ALA A 954 REMARK 465 ILE A 955 REMARK 465 PRO A 956 REMARK 465 VAL A 957 REMARK 465 ASP A 958 REMARK 465 LEU A 959 REMARK 465 LYS A 960 REMARK 465 ARG A 961 REMARK 465 ARG A 962 REMARK 465 LEU A 963 REMARK 465 ASP A 964 REMARK 465 SER A 965 REMARK 465 ILE A 966 REMARK 465 THR A 967 REMARK 465 SER A 968 REMARK 465 SER A 969 REMARK 465 GLN A 970 REMARK 465 SER A 971 REMARK 465 SER A 972 REMARK 465 ALA A 973 REMARK 465 SER A 974 REMARK 465 SER A 975 REMARK 465 GLY A 976 REMARK 465 PHE A 977 REMARK 465 VAL A 978 REMARK 465 GLU A 979 REMARK 465 GLU A 980 REMARK 465 LYS A 981 REMARK 465 SER A 982 REMARK 465 LEU A 983 REMARK 465 SER A 984 REMARK 465 ASP A 985 REMARK 465 VAL A 986 REMARK 465 GLU A 987 REMARK 465 GLU A 988 REMARK 465 GLU A 989 REMARK 465 GLU A 990 REMARK 465 ALA A 991 REMARK 465 PRO A 992 REMARK 465 GLU A 993 REMARK 465 ASP A 994 REMARK 465 LEU A 995 REMARK 465 GLY A 1063 REMARK 465 ASP A 1064 REMARK 465 GLN A 1169 REMARK 465 GLN A 1170 REMARK 465 ASP A 1171 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 THR A 875 -169.87 -120.17 REMARK 500 ARG A1027 -9.06 78.47 REMARK 500 ASP A1028 47.07 -149.04 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 BPK A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2002 DBREF 3VHK A 806 1171 UNP P35968 VGFR2_HUMAN 806 1171 SEQADV 3VHK GLY A 804 UNP P35968 EXPRESSION TAG SEQADV 3VHK ALA A 805 UNP P35968 EXPRESSION TAG SEQRES 1 A 368 GLY ALA MET ASP PRO ASP GLU LEU PRO LEU ASP GLU HIS SEQRES 2 A 368 CYS GLU ARG LEU PRO TYR ASP ALA SER LYS TRP GLU PHE SEQRES 3 A 368 PRO ARG ASP ARG LEU LYS LEU GLY LYS PRO LEU GLY ARG SEQRES 4 A 368 GLY ALA PHE GLY GLN VAL ILE GLU ALA ASP ALA PHE GLY SEQRES 5 A 368 ILE ASP LYS THR ALA THR CYS ARG THR VAL ALA VAL LYS SEQRES 6 A 368 MET LEU LYS GLU GLY ALA THR HIS SER GLU HIS ARG ALA SEQRES 7 A 368 LEU MET SER GLU LEU LYS ILE LEU ILE HIS ILE GLY HIS SEQRES 8 A 368 HIS LEU ASN VAL VAL ASN LEU LEU GLY ALA CYS THR LYS SEQRES 9 A 368 PRO GLY GLY PRO LEU MET VAL ILE VAL GLU PHE CYS LYS SEQRES 10 A 368 PHE GLY ASN LEU SER THR TYR LEU ARG SER LYS ARG ASN SEQRES 11 A 368 GLU PHE VAL PRO TYR LYS THR LYS GLY ALA ARG PHE ARG SEQRES 12 A 368 GLN GLY LYS ASP TYR VAL GLY ALA ILE PRO VAL ASP LEU SEQRES 13 A 368 LYS ARG ARG LEU ASP SER ILE THR SER SER GLN SER SER SEQRES 14 A 368 ALA SER SER GLY PHE VAL GLU GLU LYS SER LEU SER ASP SEQRES 15 A 368 VAL GLU GLU GLU GLU ALA PRO GLU ASP LEU TYR LYS ASP SEQRES 16 A 368 PHE LEU THR LEU GLU HIS LEU ILE CYS TYR SER PHE GLN SEQRES 17 A 368 VAL ALA LYS GLY MET GLU PHE LEU ALA SER ARG LYS CYS SEQRES 18 A 368 ILE HIS ARG ASP LEU ALA ALA ARG ASN ILE LEU LEU SER SEQRES 19 A 368 GLU LYS ASN VAL VAL LYS ILE CYS ASP PHE GLY LEU ALA SEQRES 20 A 368 ARG ASP ILE TYR LYS ASP PRO ASP TYR VAL ARG LYS GLY SEQRES 21 A 368 ASP ALA ARG LEU PRO LEU LYS TRP MET ALA PRO GLU THR SEQRES 22 A 368 ILE PHE ASP ARG VAL TYR THR ILE GLN SER ASP VAL TRP SEQRES 23 A 368 SER PHE GLY VAL LEU LEU TRP GLU ILE PHE SER LEU GLY SEQRES 24 A 368 ALA SER PRO TYR PRO GLY VAL LYS ILE ASP GLU GLU PHE SEQRES 25 A 368 CYS ARG ARG LEU LYS GLU GLY THR ARG MET ARG ALA PRO SEQRES 26 A 368 ASP TYR THR THR PRO GLU MET TYR GLN THR MET LEU ASP SEQRES 27 A 368 CYS TRP HIS GLY GLU PRO SER GLN ARG PRO THR PHE SER SEQRES 28 A 368 GLU LEU VAL GLU HIS LEU GLY ASN LEU LEU GLN ALA ASN SEQRES 29 A 368 ALA GLN GLN ASP HET BPK A2001 22 HET EDO A2002 4 HETNAM BPK {3-[(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL) HETNAM 2 BPK METHOXY]PHENYL}METHANOL HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 BPK C18 H17 N O3 FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *42(H2 O) HELIX 1 1 HIS A 816 LEU A 820 5 5 HELIX 2 2 ASP A 823 GLU A 828 1 6 HELIX 3 3 PRO A 830 ASP A 832 5 3 HELIX 4 4 THR A 875 GLY A 893 1 19 HELIX 5 5 ASN A 923 LYS A 931 1 9 HELIX 6 6 THR A 1001 ARG A 1022 1 22 HELIX 7 7 ALA A 1030 ARG A 1032 5 3 HELIX 8 8 GLU A 1038 ASN A 1040 5 3 HELIX 9 9 PHE A 1047 ARG A 1051 5 5 HELIX 10 10 PRO A 1068 MET A 1072 5 5 HELIX 11 11 ALA A 1073 PHE A 1078 1 6 HELIX 12 12 THR A 1083 PHE A 1099 1 17 HELIX 13 13 ASP A 1112 GLU A 1121 1 10 HELIX 14 14 THR A 1132 TRP A 1143 1 12 HELIX 15 15 GLU A 1146 ARG A 1150 5 5 HELIX 16 16 THR A 1152 ALA A 1168 1 17 SHEET 1 A 5 LEU A 834 ARG A 842 0 SHEET 2 A 5 GLY A 846 PHE A 854 -1 O VAL A 848 N LEU A 840 SHEET 3 A 5 CYS A 862 LEU A 870 -1 O VAL A 867 N ILE A 849 SHEET 4 A 5 MET A 913 GLU A 917 -1 O VAL A 914 N LYS A 868 SHEET 5 A 5 LEU A 901 CYS A 905 -1 N LEU A 902 O ILE A 915 SHEET 1 B 2 ILE A1034 LEU A1036 0 SHEET 2 B 2 VAL A1042 ILE A1044 -1 O LYS A1043 N LEU A1035 SITE 1 AC1 8 VAL A 848 LYS A 868 GLU A 885 LEU A 889 SITE 2 AC1 8 VAL A 916 CYS A1045 ASP A1046 PHE A1047 SITE 1 AC2 3 GLU A 917 CYS A 919 LEU A1035 CRYST1 135.719 56.354 51.875 90.00 95.61 90.00 C 1 2 1 4 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 0.007368 0.000000 0.000723 0.00000 SCALE2 0.000000 0.017745 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019370 0.00000