HEADER TRANSFERASE 31-MAY-09 3HNG TITLE CRYSTAL STRUCTURE OF VEGFR1 IN COMPLEX WITH N-(4-CHLOROPHENYL)-2- TITLE 2 ((PYRIDIN-4-YLMETHYL)AMINO)BENZAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN, UNP RESIDUES 801-1158; COMPND 5 SYNONYM: VEGFR-1, VASCULAR PERMEABILITY FACTOR RECEPTOR, TYROSINE- COMPND 6 PROTEIN KINASE RECEPTOR FLT, FLT-1, TYROSINE-PROTEIN KINASE FRT, FMS- COMPND 7 LIKE TYROSINE KINASE 1; COMPND 8 EC: 2.7.10.1; COMPND 9 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: FLT1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PRARE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC-BSA4 KEYWDS RECEPTOR TYROSINE KINASE, VEGFR1, FLT1, KINASE DOMAIN, INHIBITOR, KEYWDS 2 ACTIVATION LOOP, VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR, KEYWDS 3 STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, SGC KEYWDS 4 STOCKHOLM, ANGIOGENESIS, ATP-BINDING, CELL MEMBRANE, DEVELOPMENTAL KEYWDS 5 PROTEIN, DIFFERENTIATION, DISULFIDE BOND, GLYCOPROTEIN, KEYWDS 6 IMMUNOGLOBULIN DOMAIN, KINASE, MEMBRANE, NUCLEOTIDE-BINDING, KEYWDS 7 PHOSPHOPROTEIN, RECEPTOR, SECRETED, TRANSFERASE, TRANSMEMBRANE, KEYWDS 8 TYROSINE-PROTEIN KINASE EXPDTA X-RAY DIFFRACTION AUTHOR L.TRESAUGUES,A.ROOS,C.H.ARROWSMITH,H.BERGLUND,C.BOUNTRA,R.COLLINS, AUTHOR 2 A.M.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND,M.HAMMARSTROM,A.JOHANSSON, AUTHOR 3 I.JOHANSSON,T.KARLBERG,T.KOTENYOVA,M.MOCHE,T.NYMAN,C.PERSSON, AUTHOR 4 T.KRAGH-NIELSEN,A.KOTZCH,J.SAGEMARK,H.SCHUELER,P.SCHUTZ,M.I.SIPONEN, AUTHOR 5 L.SVENSSON,A.G.THORSELL,S.VAN DER BERG,J.WEIGELT,M.WELIN, AUTHOR 6 M.WISNIEWSKA,P.NORDLUND,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 01-NOV-23 3HNG 1 REMARK SEQADV REVDAT 2 13-JUL-11 3HNG 1 VERSN REVDAT 1 30-JUN-09 3HNG 0 JRNL AUTH L.TRESAUGUES,A.ROOS,C.H.ARROWSMITH,H.BERGLUND,C.BOUNTRA, JRNL AUTH 2 R.COLLINS,A.M.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND, JRNL AUTH 3 M.HAMMARSTROM,A.JOHANSSON,I.JOHANSSON,T.KARLBERG, JRNL AUTH 4 T.KOTENYOVA,M.MOCHE,T.NYMAN,C.PERSSON,T.KRAGH-NIELSEN, JRNL AUTH 5 A.KOTZCH,J.SAGEMARK,H.SCHUELER,P.SCHUTZ,M.I.SIPONEN, JRNL AUTH 6 L.SVENSSON,A.G.THORSELL,S.VAN DER BERG,J.WEIGELT,M.WELIN, JRNL AUTH 7 M.WISNIEWSKA,P.NORDLUND JRNL TITL CRYSTAL STRUCTURE OF VEGFR1 IN COMPLEX WITH JRNL TITL 2 N-(4-CHLOROPHENYL)-2-((PYRIDIN-4-YLMETHYL)AMINO)BENZAMIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10998 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 551 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 798 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.3350 REMARK 3 BIN FREE R VALUE SET COUNT : 33 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2290 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 33 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 65.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : 1.14000 REMARK 3 B33 (A**2) : -1.23000 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): 0.654 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.331 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.232 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 23.981 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.891 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2374 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2186 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3196 ; 1.460 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5086 ; 0.640 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 286 ; 7.077 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;32.976 ;23.168 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 433 ;19.825 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;20.508 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 343 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2583 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 495 ; 0.000 ; 0.021 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): 1434 ; 0.547 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 584 ; 0.094 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2304 ; 1.086 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 940 ; 1.584 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 891 ; 2.727 ; 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 : 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 803 A 818 REMARK 3 ORIGIN FOR THE GROUP (A): 12.2550 33.5610 34.9560 REMARK 3 T TENSOR REMARK 3 T11: 0.9245 T22: 1.0044 REMARK 3 T33: 1.3602 T12: -0.3877 REMARK 3 T13: -0.0829 T23: 0.1977 REMARK 3 L TENSOR REMARK 3 L11: 5.8434 L22: 5.9662 REMARK 3 L33: 8.2998 L12: 5.1424 REMARK 3 L13: -6.7994 L23: -5.8046 REMARK 3 S TENSOR REMARK 3 S11: 1.5017 S12: -0.1379 S13: 0.6433 REMARK 3 S21: 1.5686 S22: -0.4986 S23: -0.7771 REMARK 3 S31: -2.0899 S32: 0.6879 S33: -1.0031 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 819 A 925 REMARK 3 ORIGIN FOR THE GROUP (A): 3.7040 16.4860 37.9550 REMARK 3 T TENSOR REMARK 3 T11: 0.0397 T22: 0.0860 REMARK 3 T33: 0.0582 T12: -0.0047 REMARK 3 T13: 0.0104 T23: 0.0277 REMARK 3 L TENSOR REMARK 3 L11: 3.1897 L22: 1.3592 REMARK 3 L33: 4.9452 L12: -0.4202 REMARK 3 L13: 0.7073 L23: 0.2763 REMARK 3 S TENSOR REMARK 3 S11: 0.1324 S12: -0.2282 S13: -0.0083 REMARK 3 S21: 0.0456 S22: -0.1085 S23: 0.0412 REMARK 3 S31: 0.2883 S32: -0.0291 S33: -0.0239 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 992 A 1158 REMARK 3 ORIGIN FOR THE GROUP (A): 5.6020 17.9350 15.6330 REMARK 3 T TENSOR REMARK 3 T11: 0.1364 T22: 0.1750 REMARK 3 T33: 0.0167 T12: 0.0289 REMARK 3 T13: -0.0057 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 3.9522 L22: 3.7270 REMARK 3 L33: 5.7472 L12: 0.2827 REMARK 3 L13: 0.6757 L23: 0.3388 REMARK 3 S TENSOR REMARK 3 S11: 0.0015 S12: 0.5707 S13: 0.0520 REMARK 3 S21: -0.3207 S22: 0.0732 S23: -0.1965 REMARK 3 S31: 0.2258 S32: 0.7144 S33: -0.0747 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 REMARK 4 REMARK 4 3HNG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053349. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93300 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE(220) REMARK 200 OPTICS : TOROIDAL ZERODUR MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11958 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 44.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.07800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.50600 REMARK 200 R SYM FOR SHELL (I) : 0.44100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 2QU5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M POTASSIUM FORMATE, 20% PEG 3350, REMARK 280 PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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 -X,Y,-Z REMARK 290 4555 X,-Y,-Z 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 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+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 1.000000 0.000000 0.000000 29.02000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.57500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 98.01000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.02000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.57500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 98.01000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.02000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.57500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 98.01000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.02000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.57500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 98.01000 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 SER A 799 REMARK 465 MET A 800 REMARK 465 PRO A 801 REMARK 465 ASP A 802 REMARK 465 LEU A 813 REMARK 465 ASP A 926 REMARK 465 LEU A 927 REMARK 465 PHE A 928 REMARK 465 PHE A 929 REMARK 465 LEU A 930 REMARK 465 ASN A 931 REMARK 465 LYS A 932 REMARK 465 ASP A 933 REMARK 465 ALA A 934 REMARK 465 ALA A 935 REMARK 465 LEU A 936 REMARK 465 HIS A 937 REMARK 465 MET A 938 REMARK 465 GLU A 939 REMARK 465 PRO A 940 REMARK 465 LYS A 941 REMARK 465 LYS A 942 REMARK 465 GLU A 943 REMARK 465 LYS A 944 REMARK 465 MET A 945 REMARK 465 GLU A 946 REMARK 465 PRO A 947 REMARK 465 GLY A 948 REMARK 465 LEU A 949 REMARK 465 GLU A 950 REMARK 465 GLN A 951 REMARK 465 GLY A 952 REMARK 465 LYS A 953 REMARK 465 LYS A 954 REMARK 465 PRO A 955 REMARK 465 ARG A 956 REMARK 465 LEU A 957 REMARK 465 ASP A 958 REMARK 465 SER A 959 REMARK 465 VAL A 960 REMARK 465 THR A 961 REMARK 465 SER A 962 REMARK 465 SER A 963 REMARK 465 GLU A 964 REMARK 465 SER A 965 REMARK 465 PHE A 966 REMARK 465 ALA A 967 REMARK 465 SER A 968 REMARK 465 SER A 969 REMARK 465 GLY A 970 REMARK 465 PHE A 971 REMARK 465 GLN A 972 REMARK 465 GLU A 973 REMARK 465 ASP A 974 REMARK 465 LYS A 975 REMARK 465 SER A 976 REMARK 465 LEU A 977 REMARK 465 SER A 978 REMARK 465 ASP A 979 REMARK 465 VAL A 980 REMARK 465 GLU A 981 REMARK 465 GLU A 982 REMARK 465 GLU A 983 REMARK 465 GLU A 984 REMARK 465 ASP A 985 REMARK 465 SER A 986 REMARK 465 ASP A 987 REMARK 465 GLY A 988 REMARK 465 PHE A 989 REMARK 465 TYR A 990 REMARK 465 GLY A 1057 REMARK 465 ASP A 1058 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 ARG A 812 NE CZ NH1 NH2 REMARK 470 LYS A 991 CG CD CE NZ REMARK 470 ARG A1055 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1056 CG CD CE NZ REMARK 470 ARG A1139 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH2 ARG A 1146 OE2 GLU A 1152 2565 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 810 39.73 -87.63 REMARK 500 ASP A 816 73.12 -108.28 REMARK 500 SER A 818 -31.33 -37.64 REMARK 500 ILE A 885 -59.86 -122.96 REMARK 500 LYS A 900 125.88 -30.64 REMARK 500 ARG A1021 -7.08 79.26 REMARK 500 ASP A1022 50.19 -152.76 REMARK 500 ALA A1024 165.73 177.59 REMARK 500 SER A1031 -161.99 -107.68 REMARK 500 MET A1105 77.41 -110.09 REMARK 500 ASP A1106 -167.81 -119.89 REMARK 500 CYS A1110 -72.25 -70.73 REMARK 500 SER A1111 -38.62 -35.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 886 HIS A 887 42.36 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 8ST A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 3035 DBREF 3HNG A 801 1158 UNP P17948 VGFR1_HUMAN 801 1158 SEQADV 3HNG SER A 799 UNP P17948 EXPRESSION TAG SEQADV 3HNG MET A 800 UNP P17948 EXPRESSION TAG SEQRES 1 A 360 SER MET PRO ASP GLU VAL PRO LEU ASP GLU GLN CYS GLU SEQRES 2 A 360 ARG LEU PRO TYR ASP ALA SER LYS TRP GLU PHE ALA ARG SEQRES 3 A 360 GLU ARG LEU LYS LEU GLY LYS SER LEU GLY ARG GLY ALA SEQRES 4 A 360 PHE GLY LYS VAL VAL GLN ALA SER ALA PHE GLY ILE LYS SEQRES 5 A 360 LYS SER PRO THR CYS ARG THR VAL ALA VAL LYS MET LEU SEQRES 6 A 360 LYS GLU GLY ALA THR ALA SER GLU TYR LYS ALA LEU MET SEQRES 7 A 360 THR GLU LEU LYS ILE LEU THR HIS ILE GLY HIS HIS LEU SEQRES 8 A 360 ASN VAL VAL ASN LEU LEU GLY ALA CYS THR LYS GLN GLY SEQRES 9 A 360 GLY PRO LEU MET VAL ILE VAL GLU TYR CYS LYS TYR GLY SEQRES 10 A 360 ASN LEU SER ASN TYR LEU LYS SER LYS ARG ASP LEU PHE SEQRES 11 A 360 PHE LEU ASN LYS ASP ALA ALA LEU HIS MET GLU PRO LYS SEQRES 12 A 360 LYS GLU LYS MET GLU PRO GLY LEU GLU GLN GLY LYS LYS SEQRES 13 A 360 PRO ARG LEU ASP SER VAL THR SER SER GLU SER PHE ALA SEQRES 14 A 360 SER SER GLY PHE GLN GLU ASP LYS SER LEU SER ASP VAL SEQRES 15 A 360 GLU GLU GLU GLU ASP SER ASP GLY PHE TYR LYS GLU PRO SEQRES 16 A 360 ILE THR MET GLU ASP LEU ILE SER TYR SER PHE GLN VAL SEQRES 17 A 360 ALA ARG GLY MET GLU PHE LEU SER SER ARG LYS CYS ILE SEQRES 18 A 360 HIS ARG ASP LEU ALA ALA ARG ASN ILE LEU LEU SER GLU SEQRES 19 A 360 ASN ASN VAL VAL LYS ILE CYS ASP PHE GLY LEU ALA ARG SEQRES 20 A 360 ASP ILE TYR LYS ASN PRO ASP TYR VAL ARG LYS GLY ASP SEQRES 21 A 360 THR ARG LEU PRO LEU LYS TRP MET ALA PRO GLU SER ILE SEQRES 22 A 360 PHE ASP LYS ILE TYR SER THR LYS SER ASP VAL TRP SER SEQRES 23 A 360 TYR GLY VAL LEU LEU TRP GLU ILE PHE SER LEU GLY GLY SEQRES 24 A 360 SER PRO TYR PRO GLY VAL GLN MET ASP GLU ASP PHE CYS SEQRES 25 A 360 SER ARG LEU ARG GLU GLY MET ARG MET ARG ALA PRO GLU SEQRES 26 A 360 TYR SER THR PRO GLU ILE TYR GLN ILE MET LEU ASP CYS SEQRES 27 A 360 TRP HIS ARG ASP PRO LYS GLU ARG PRO ARG PHE ALA GLU SEQRES 28 A 360 LEU VAL GLU LYS LEU GLY ASP LEU LEU HET 8ST A2001 24 HET CL A3035 1 HETNAM 8ST N-(4-CHLOROPHENYL)-2-[(PYRIDIN-4-YLMETHYL) HETNAM 2 8ST AMINO]BENZAMIDE HETNAM CL CHLORIDE ION FORMUL 2 8ST C19 H16 CL N3 O FORMUL 3 CL CL 1- FORMUL 4 HOH *33(H2 O) HELIX 1 1 PRO A 805 CYS A 810 1 6 HELIX 2 2 ASP A 816 GLU A 821 1 6 HELIX 3 3 ALA A 823 GLU A 825 5 3 HELIX 4 4 ILE A 849 SER A 852 5 4 HELIX 5 5 THR A 868 HIS A 884 1 17 HELIX 6 6 ASN A 916 SER A 923 1 8 HELIX 7 7 THR A 995 SER A 1015 1 21 HELIX 8 8 ALA A 1024 ARG A 1026 5 3 HELIX 9 9 GLU A 1032 ASN A 1034 5 3 HELIX 10 10 PHE A 1041 ARG A 1045 5 5 HELIX 11 11 PRO A 1062 MET A 1066 5 5 HELIX 12 12 ALA A 1067 LYS A 1074 1 8 HELIX 13 13 SER A 1077 SER A 1094 1 18 HELIX 14 14 ASP A 1106 ARG A 1114 1 9 HELIX 15 15 THR A 1126 TRP A 1137 1 12 HELIX 16 16 ASP A 1140 ARG A 1144 5 5 HELIX 17 17 ARG A 1146 LEU A 1158 1 13 SHEET 1 A 5 LEU A 827 ARG A 835 0 SHEET 2 A 5 GLY A 839 PHE A 847 -1 O VAL A 841 N LEU A 833 SHEET 3 A 5 CYS A 855 LEU A 863 -1 O ARG A 856 N ALA A 846 SHEET 4 A 5 MET A 906 GLU A 910 -1 O VAL A 909 N ALA A 859 SHEET 5 A 5 LEU A 894 CYS A 898 -1 N LEU A 895 O ILE A 908 SHEET 1 B 2 ILE A1028 LEU A1030 0 SHEET 2 B 2 VAL A1036 ILE A1038 -1 O LYS A1037 N LEU A1029 SITE 1 AC1 12 LYS A 861 GLU A 878 VAL A 907 VAL A 909 SITE 2 AC1 12 GLU A 910 TYR A 911 CYS A 912 LEU A1013 SITE 3 AC1 12 LEU A1029 ILE A1038 CYS A1039 ASP A1040 SITE 1 AC2 1 LYS A 850 CRYST1 58.040 71.150 196.020 90.00 90.00 90.00 I 2 2 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 0.017229 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014055 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005102 0.00000