PDB Short entry for 3C7Q HEADER TRANSFERASE 08-FEB-08 3C7Q TITLE STRUCTURE OF VEGFR2 KINASE DOMAIN IN COMPLEX WITH BIBF1120 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN; COMPND 5 SYNONYM: VEGFR-2, KINASE INSERT DOMAIN RECEPTOR, PROTEIN-TYROSINE COMPND 6 KINASE RECEPTOR FLK-1, CD309 ANTIGEN; 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_STRAIN: HIGH5; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 12 EXPRESSION_SYSTEM_VECTOR: PFB1 KEYWDS ALPHA BETA, ANGIOGENESIS, ATP-BINDING, DEVELOPMENTAL PROTEIN, KEYWDS 2 DIFFERENTIATION, GLYCOPROTEIN, HOST-VIRUS INTERACTION, KEYWDS 3 IMMUNOGLOBULIN DOMAIN, KINASE, MEMBRANE, NUCLEOTIDE-BINDING, KEYWDS 4 PHOSPHOPROTEIN, RECEPTOR, TRANSFERASE, TRANSMEMBRANE, TYROSINE- KEYWDS 5 PROTEIN KINASE EXPDTA X-RAY DIFFRACTION AUTHOR F.HILBERG,G.J.ROTH,M.KRSSAK,S.KAUTSCHITSCH,W.SOMMERGRUBER,U.TONTSCH- AUTHOR 2 GRUNT,P.GARIN-CHESA,G.BADER,A.ZOEPHEL,J.QUANT,A.HECKEL,W.J.RETTIG REVDAT 5 15-NOV-23 3C7Q 1 REMARK REVDAT 4 01-NOV-23 3C7Q 1 REMARK SEQADV LINK REVDAT 3 25-OCT-17 3C7Q 1 REMARK REVDAT 2 13-JUL-11 3C7Q 1 VERSN REVDAT 1 23-DEC-08 3C7Q 0 JRNL AUTH F.HILBERG,G.J.ROTH,M.KRSSAK,S.KAUTSCHITSCH,W.SOMMERGRUBER, JRNL AUTH 2 U.TONTSCH-GRUNT,P.GARIN-CHESA,G.BADER,A.ZOEPHEL,J.QUANT, JRNL AUTH 3 A.HECKEL,W.J.RETTIG JRNL TITL BIBF 1120: TRIPLE ANGIOKINASE INHIBITOR WITH SUSTAINED JRNL TITL 2 RECEPTOR BLOCKADE AND GOOD ANTITUMOR EFFICACY. JRNL REF CANCER RES. V. 68 4774 2008 JRNL REFN ISSN 0008-5472 JRNL PMID 18559524 JRNL DOI 10.1158/0008-5472.CAN-07-6307 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 19934 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1050 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1447 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2770 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.4020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2362 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 206 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 32.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.87000 REMARK 3 B22 (A**2) : 2.84000 REMARK 3 B33 (A**2) : -1.97000 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): 0.243 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.215 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.194 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.470 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2455 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1694 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3323 ; 1.633 ; 2.003 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4090 ; 0.997 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 288 ; 8.311 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;36.284 ;22.991 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 405 ;16.389 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.038 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 350 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2652 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 515 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 561 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1787 ; 0.200 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1163 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1255 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 149 ; 0.181 ; 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): 25 ; 0.197 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 51 ; 0.220 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.267 ; 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): 1870 ; 1.184 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 585 ; 0.155 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2325 ; 1.354 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1220 ; 1.789 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 998 ; 2.529 ; 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 : 1 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 819 A 1171 REMARK 3 ORIGIN FOR THE GROUP (A): 24.2360 56.6750 24.8540 REMARK 3 T TENSOR REMARK 3 T11: -0.0329 T22: -0.0264 REMARK 3 T33: -0.0113 T12: 0.0304 REMARK 3 T13: -0.0095 T23: -0.0198 REMARK 3 L TENSOR REMARK 3 L11: 0.3213 L22: 0.2557 REMARK 3 L33: 1.2602 L12: 0.0304 REMARK 3 L13: -0.3528 L23: 0.2771 REMARK 3 S TENSOR REMARK 3 S11: 0.0005 S12: 0.0572 S13: -0.0733 REMARK 3 S21: 0.0138 S22: -0.0414 S23: 0.0071 REMARK 3 S31: -0.0557 S32: -0.1179 S33: 0.0409 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 3C7Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000046446. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 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) : 0.9799 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23933 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 98.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.55900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: 1VR2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 2.1M AMMONIUM SULPHATE, 3% REMARK 280 PEG MME 550, 10MM BETA-MERCAPTOETHANOL, PH 7.4, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 19.12500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.11000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.22000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.11000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.12500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.22000 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 SER 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 ASP A 814 REMARK 465 GLU A 815 REMARK 465 HIS A 816 REMARK 465 CYS A 817 REMARK 465 GLU A 818 REMARK 465 PRO A 992 REMARK 465 GLU A 993 REMARK 465 ASP A 994 REMARK 465 LEU A 995 REMARK 465 TYR A 996 REMARK 465 LYS A 997 REMARK 465 GLY A 1048 REMARK 465 LEU A 1049 REMARK 465 ALA A 1050 REMARK 465 ARG A 1051 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 835 CG CD CE NZ REMARK 480 LYS A 907 NZ REMARK 480 ARG A 1061 NE CZ NH1 NH2 REMARK 480 LYS A 1062 CG CD CE NZ REMARK 480 LYS A 1110 CB CG CD CE NZ REMARK 480 GLU A 1113 CB CG CD OE1 OE2 REMARK 480 GLU A 1114 CG CD OE1 OE2 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 O ASP A 1064 O HOH A 1376 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 O1 SO4 A 1 O HOH A 1275 1455 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 907 CE LYS A 907 NZ -0.177 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A1058 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES 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 LYS A 858 -9.57 73.79 REMARK 500 ALA A 860 43.79 -86.81 REMARK 500 ALA A 874 89.63 73.57 REMARK 500 ARG A1027 -6.86 82.47 REMARK 500 ASP A1028 49.99 -157.14 REMARK 500 SER A1037 -168.43 -106.98 REMARK 500 ILE A1053 -7.23 -151.78 REMARK 500 PTR A1054 -89.07 0.55 REMARK 500 ASP A1064 0.93 -65.86 REMARK 500 ILE A1111 78.16 -101.56 REMARK 500 ASP A1112 -167.16 -109.64 REMARK 500 TRP A1143 32.55 -96.98 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 ILE A 1053 PTR A 1054 77.53 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 SO4 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XIN A 1172 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE ARE DELETIONS T940-A991 AND RESIDUE NUMBERS 940-991 ARE REMARK 999 SIMPLY SKIPPED. DBREF 3C7Q A 806 1171 UNP P35968 VGFR2_HUMAN 806 1171 SEQADV 3C7Q GLY A 804 UNP P35968 EXPRESSION TAG SEQADV 3C7Q SER A 805 UNP P35968 EXPRESSION TAG SEQADV 3C7Q A UNP P35968 THR 940 DELETION SEQADV 3C7Q A UNP P35968 LYS 941 DELETION SEQADV 3C7Q A UNP P35968 GLY 942 DELETION SEQADV 3C7Q A UNP P35968 ALA 943 DELETION SEQADV 3C7Q A UNP P35968 ARG 944 DELETION SEQADV 3C7Q A UNP P35968 PHE 945 DELETION SEQADV 3C7Q A UNP P35968 ARG 946 DELETION SEQADV 3C7Q A UNP P35968 GLN 947 DELETION SEQADV 3C7Q A UNP P35968 GLY 948 DELETION SEQADV 3C7Q A UNP P35968 LYS 949 DELETION SEQADV 3C7Q A UNP P35968 ASP 950 DELETION SEQADV 3C7Q A UNP P35968 TYR 951 DELETION SEQADV 3C7Q A UNP P35968 VAL 952 DELETION SEQADV 3C7Q A UNP P35968 GLY 953 DELETION SEQADV 3C7Q A UNP P35968 ALA 954 DELETION SEQADV 3C7Q A UNP P35968 ILE 955 DELETION SEQADV 3C7Q A UNP P35968 PRO 956 DELETION SEQADV 3C7Q A UNP P35968 VAL 957 DELETION SEQADV 3C7Q A UNP P35968 ASP 958 DELETION SEQADV 3C7Q A UNP P35968 LEU 959 DELETION SEQADV 3C7Q A UNP P35968 LYS 960 DELETION SEQADV 3C7Q A UNP P35968 ARG 961 DELETION SEQADV 3C7Q A UNP P35968 ARG 962 DELETION SEQADV 3C7Q A UNP P35968 LEU 963 DELETION SEQADV 3C7Q A UNP P35968 ASP 964 DELETION SEQADV 3C7Q A UNP P35968 SER 965 DELETION SEQADV 3C7Q A UNP P35968 ILE 966 DELETION SEQADV 3C7Q A UNP P35968 THR 967 DELETION SEQADV 3C7Q A UNP P35968 SER 968 DELETION SEQADV 3C7Q A UNP P35968 SER 969 DELETION SEQADV 3C7Q A UNP P35968 GLN 970 DELETION SEQADV 3C7Q A UNP P35968 SER 971 DELETION SEQADV 3C7Q A UNP P35968 SER 972 DELETION SEQADV 3C7Q A UNP P35968 ALA 973 DELETION SEQADV 3C7Q A UNP P35968 SER 974 DELETION SEQADV 3C7Q A UNP P35968 SER 975 DELETION SEQADV 3C7Q A UNP P35968 GLY 976 DELETION SEQADV 3C7Q A UNP P35968 PHE 977 DELETION SEQADV 3C7Q A UNP P35968 VAL 978 DELETION SEQADV 3C7Q A UNP P35968 GLU 979 DELETION SEQADV 3C7Q A UNP P35968 GLU 980 DELETION SEQADV 3C7Q A UNP P35968 LYS 981 DELETION SEQADV 3C7Q A UNP P35968 SER 982 DELETION SEQADV 3C7Q A UNP P35968 LEU 983 DELETION SEQADV 3C7Q A UNP P35968 SER 984 DELETION SEQADV 3C7Q A UNP P35968 ASP 985 DELETION SEQADV 3C7Q A UNP P35968 VAL 986 DELETION SEQADV 3C7Q A UNP P35968 GLU 987 DELETION SEQADV 3C7Q A UNP P35968 GLU 988 DELETION SEQADV 3C7Q A UNP P35968 GLU 989 DELETION SEQADV 3C7Q A UNP P35968 GLU 990 DELETION SEQADV 3C7Q A UNP P35968 ALA 991 DELETION SEQRES 1 A 316 GLY SER MET ASP PRO ASP GLU LEU PRO LEU ASP GLU HIS SEQRES 2 A 316 CYS GLU ARG LEU PRO TYR ASP ALA SER LYS TRP GLU PHE SEQRES 3 A 316 PRO ARG ASP ARG LEU LYS LEU GLY LYS PRO LEU GLY ARG SEQRES 4 A 316 GLY ALA PHE GLY GLN VAL ILE GLU ALA ASP ALA PHE GLY SEQRES 5 A 316 ILE ASP LYS THR ALA THR CME ARG THR VAL ALA VAL LYS SEQRES 6 A 316 MET LEU LYS GLU GLY ALA THR HIS SER GLU HIS ARG ALA SEQRES 7 A 316 LEU MET SER GLU LEU LYS ILE LEU ILE HIS ILE GLY HIS SEQRES 8 A 316 HIS LEU ASN VAL VAL ASN LEU LEU GLY ALA CYS THR LYS SEQRES 9 A 316 PRO GLY GLY PRO LEU MET VAL ILE VAL GLU PHE CYS LYS SEQRES 10 A 316 PHE GLY ASN LEU SER THR TYR LEU ARG SER LYS ARG ASN SEQRES 11 A 316 GLU PHE VAL PRO TYR LYS PRO GLU ASP LEU TYR LYS ASP SEQRES 12 A 316 PHE LEU THR LEU GLU HIS LEU ILE CME TYR SER PHE GLN SEQRES 13 A 316 VAL ALA LYS GLY MET GLU PHE LEU ALA SER ARG LYS CME SEQRES 14 A 316 ILE HIS ARG ASP LEU ALA ALA ARG ASN ILE LEU LEU SER SEQRES 15 A 316 GLU LYS ASN VAL VAL LYS ILE CYS ASP PHE GLY LEU ALA SEQRES 16 A 316 ARG ASP ILE PTR LYS ASP PRO ASP PTR VAL ARG LYS GLY SEQRES 17 A 316 ASP ALA ARG LEU PRO LEU LYS TRP MET ALA PRO GLU THR SEQRES 18 A 316 ILE PHE ASP ARG VAL TYR THR ILE GLN SER ASP VAL TRP SEQRES 19 A 316 SER PHE GLY VAL LEU LEU TRP GLU ILE PHE SER LEU GLY SEQRES 20 A 316 ALA SER PRO TYR PRO GLY VAL LYS ILE ASP GLU GLU PHE SEQRES 21 A 316 CYS ARG ARG LEU LYS GLU GLY THR ARG MET ARG ALA PRO SEQRES 22 A 316 ASP TYR THR THR PRO GLU MET TYR GLN THR MET LEU ASP SEQRES 23 A 316 CYS TRP HIS GLY GLU PRO SER GLN ARG PRO THR PHE SER SEQRES 24 A 316 GLU LEU VAL GLU HIS LEU GLY ASN LEU LEU GLN ALA ASN SEQRES 25 A 316 ALA GLN GLN ASP MODRES 3C7Q CME A 862 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE MODRES 3C7Q CME A 1007 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE MODRES 3C7Q CME A 1024 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE MODRES 3C7Q PTR A 1054 TYR O-PHOSPHOTYROSINE MODRES 3C7Q PTR A 1059 TYR O-PHOSPHOTYROSINE HET CME A 862 10 HET CME A1007 10 HET CME A1024 10 HET PTR A1054 16 HET PTR A1059 16 HET SO4 A 1 5 HET SO4 A 2 5 HET SO4 A 3 5 HET SO4 A 4 5 HET SO4 A 6 5 HET XIN A1172 40 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM PTR O-PHOSPHOTYROSINE HETNAM SO4 SULFATE ION HETNAM XIN METHYL (3Z)-3-{[(4-{METHYL[(4-METHYLPIPERAZIN-1-YL) HETNAM 2 XIN ACETYL]AMINO}PHENYL)AMINO](PHENYL)METHYLIDENE}-2-OXO- HETNAM 3 XIN 2,3-DIHYDRO-1H-INDOLE-6-CARBOXYLATE HETSYN PTR PHOSPHONOTYROSINE FORMUL 1 CME 3(C5 H11 N O3 S2) FORMUL 1 PTR 2(C9 H12 N O6 P) FORMUL 2 SO4 5(O4 S 2-) FORMUL 7 XIN C31 H33 N5 O4 FORMUL 8 HOH *206(H2 O) HELIX 1 1 ASP A 823 GLU A 828 1 6 HELIX 2 2 PRO A 830 ASP A 832 5 3 HELIX 3 3 THR A 875 GLY A 893 1 19 HELIX 4 4 LEU A 924 SER A 930 1 7 HELIX 5 5 LYS A 931 PHE A 935 5 5 HELIX 6 6 THR A 1001 ARG A 1022 1 22 HELIX 7 7 GLU A 1038 ASN A 1040 5 3 HELIX 8 8 LEU A 1067 MET A 1072 5 6 HELIX 9 9 ALA A 1073 ARG A 1080 1 8 HELIX 10 10 THR A 1083 SER A 1100 1 18 HELIX 11 11 ASP A 1112 GLY A 1122 1 11 HELIX 12 12 THR A 1132 TRP A 1143 1 12 HELIX 13 13 GLU A 1146 ARG A 1150 5 5 HELIX 14 14 THR A 1152 ALA A 1168 1 17 SHEET 1 A 5 LEU A 834 ARG A 842 0 SHEET 2 A 5 GLN A 847 PHE A 854 -1 O VAL A 848 N LEU A 840 SHEET 3 A 5 CME A 862 MET A 869 -1 O ARG A 863 N ALA A 853 SHEET 4 A 5 MET A 913 GLU A 917 -1 O VAL A 916 N ALA A 866 SHEET 5 A 5 LEU A 901 CYS A 905 -1 N LEU A 902 O ILE A 915 SHEET 1 B 3 GLY A 922 ASN A 923 0 SHEET 2 B 3 ILE A1034 LEU A1036 -1 O LEU A1036 N GLY A 922 SHEET 3 B 3 VAL A1042 ILE A1044 -1 O LYS A1043 N LEU A1035 LINK C THR A 861 N CME A 862 1555 1555 1.33 LINK C CME A 862 N ARG A 863 1555 1555 1.33 LINK C ILE A1006 N CME A1007 1555 1555 1.33 LINK C CME A1007 N TYR A1008 1555 1555 1.33 LINK C LYS A1023 N CME A1024 1555 1555 1.33 LINK C CME A1024 N ILE A1025 1555 1555 1.33 LINK C ILE A1053 N PTR A1054 1555 1555 1.33 LINK C PTR A1054 N LYS A1055 1555 1555 1.32 LINK C ASP A1058 N PTR A1059 1555 1555 1.33 LINK C PTR A1059 N VAL A1060 1555 1555 1.33 SITE 1 AC1 5 LEU A 896 GLN A1011 ILE A1053 HOH A1275 SITE 2 AC1 5 HOH A1360 SITE 1 AC2 5 ARG A1032 PHE A1047 ASP A1052 HOH A1304 SITE 2 AC2 5 HOH A1342 SITE 1 AC3 5 ILE A1111 ASN A1162 LEU A1163 ALA A1166 SITE 2 AC3 5 HOH A1197 SITE 1 AC4 3 ARG A 863 THR A 864 HOH A1238 SITE 1 AC5 2 GLU A1038 LYS A1039 SITE 1 AC6 10 LEU A 840 GLU A 850 ALA A 866 LYS A 868 SITE 2 AC6 10 GLU A 917 PHE A 918 CYS A 919 LYS A 920 SITE 3 AC6 10 LEU A1035 CYS A1045 CRYST1 38.250 94.440 96.220 90.00 90.00 90.00 P 21 21 21 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 0.026144 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010589 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010393 0.00000