PDB Short entry for 2XAC HEADER TRANSFERASE/SIGNALING PROTEIN 30-MAR-10 2XAC TITLE STRUCTURAL INSIGHTS INTO THE BINDING OF VEGF-B BY VEGFR-1D2: TITLE 2 RECOGNITION AND SPECIFICITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RECEPTOR-BINDING DOMAIN, RESIDUES 31-129; COMPND 5 SYNONYM: VEGF-B, VEGF-RELATED FACTOR, VRF; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1; COMPND 9 CHAIN: C, X; COMPND 10 FRAGMENT: DOMAIN 2, RESIDUES 129-226; COMPND 11 SYNONYM: VEGFR-1, VASCULAR PERMEABILITY FACTOR RECEPTOR, TYROSINE- COMPND 12 PROTEIN KINASE RECEPTOR FLT, TYROSINE-PROTEIN KINASE FRT, FLT-1, FMS- COMPND 13 LIKE TYROSINE KINASE 1; COMPND 14 EC: 2.7.10.1; 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: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTAGAMI B (DE3) PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-32 XA/LIC; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODONPLUS-RIPL; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS TRANSFERASE-SIGNALING PROTEIN COMPLEX, ANGIOGENESIS, CYSTEINE-KNOT KEYWDS 2 PROTEIN, MITOGEN, TRANSFERASE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.IYER,P.DARLEY,K.R.ACHARYA REVDAT 4 20-DEC-23 2XAC 1 REMARK REVDAT 3 04-AUG-10 2XAC 1 JRNL REVDAT 2 09-JUN-10 2XAC 1 JRNL REVDAT 1 19-MAY-10 2XAC 0 JRNL AUTH S.IYER,P.DARLEY,K.R.ACHARYA JRNL TITL STRUCTURAL INSIGHTS INTO THE BINDING OF VEGF-B BY VEGFR-1D2: JRNL TITL 2 RECOGNITION AND SPECIFICITY JRNL REF J.BIOL.CHEM. V. 285 23779 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20501651 JRNL DOI 10.1074/JBC.M110.130658 REMARK 2 REMARK 2 RESOLUTION. 2.71 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) : 2.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 3 NUMBER OF REFLECTIONS : 9289 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) : 0.286 REMARK 3 R VALUE (WORKING SET) : 0.282 REMARK 3 FREE R VALUE : 0.364 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 476 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) : 2.71 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.78 REMARK 3 REFLECTION IN BIN (WORKING SET) : 330 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 41.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.4450 REMARK 3 BIN FREE R VALUE SET COUNT : 18 REMARK 3 BIN FREE R VALUE : 0.5000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2974 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 33 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.06000 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): 0.606 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.519 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 25.128 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.871 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.801 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3050 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4140 ; 1.113 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 384 ; 5.803 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;40.170 ;23.534 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 537 ;17.884 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;14.663 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 475 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2246 ; 0.004 ; 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): 1928 ; 0.317 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3149 ; 0.583 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1122 ; 0.581 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 991 ; 1.034 ; 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 REMARK 4 REMARK 4 2XAC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1290043483. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11510 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.710 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 47.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER FOR MR REMARK 200 STARTING MODEL: PDB ENTRIES 2C7W AND 1FLT REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG 4000, 0.1M SODIUM CITRATE, PH REMARK 280 5.6 AND 0.2M LICL, PH 8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 32.76300 REMARK 290 SMTRY3 2 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: 6020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, X 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 HIS B 10 REMARK 465 SER X 129 REMARK 465 ASP X 130 REMARK 465 THR X 131 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 12 CB CG CD NE CZ NH1 NH2 REMARK 470 ILE A 18 CB CG1 CG2 CD1 REMARK 470 GLU A 38 CB CG CD OE1 OE2 REMARK 470 TYR A 85 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 12 CB CG CD NE CZ NH1 NH2 REMARK 470 GLU B 38 CB CG CD OE1 OE2 REMARK 470 THR B 42 CB OG1 CG2 REMARK 470 ALA B 44 CB REMARK 470 LYS B 45 CB CG CD CE NZ REMARK 470 ARG B 84 CB CG CD NE CZ NH1 NH2 REMARK 470 GLN B 89 CG CD OE1 NE2 REMARK 470 GLU B 96 CG CD OE1 OE2 REMARK 470 LYS B 108 CA C O CB CG CD CE REMARK 470 LYS B 108 NZ REMARK 470 TYR C 139 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR C 139 OH REMARK 470 LEU C 174 CB CG CD1 CD2 REMARK 470 ASP C 180 CB CG OD1 OD2 REMARK 470 LYS C 182 CB CG CD CE NZ REMARK 470 ARG C 183 CB CG CD NE CZ NH1 NH2 REMARK 470 ILE C 184 CG1 CG2 CD1 REMARK 470 GLN C 225 CB CG CD OE1 NE2 REMARK 470 THR C 226 CA C O CB OG1 CG2 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 ARG A 12 156.85 92.00 REMARK 500 ILE A 18 -66.10 110.17 REMARK 500 ALA A 24 39.92 -97.97 REMARK 500 CYS A 26 102.33 -46.60 REMARK 500 VAL A 37 109.63 -50.65 REMARK 500 GLU A 38 -47.81 137.72 REMARK 500 TYR A 85 -152.69 56.12 REMARK 500 ARG B 12 -129.25 114.00 REMARK 500 ARG B 23 49.42 -82.85 REMARK 500 ALA B 24 6.47 -160.41 REMARK 500 LEU B 35 44.19 -97.21 REMARK 500 GLU B 38 -158.47 -74.18 REMARK 500 THR B 42 -134.66 18.64 REMARK 500 ALA B 44 113.60 88.42 REMARK 500 LYS B 45 -148.79 151.66 REMARK 500 ARG B 84 -145.81 173.24 REMARK 500 PRO B 86 -58.64 -124.87 REMARK 500 TYR C 139 -97.70 105.89 REMARK 500 SER C 140 70.10 44.61 REMARK 500 PRO C 157 33.59 -76.80 REMARK 500 THR C 161 -86.82 -74.35 REMARK 500 LYS C 170 -169.20 -113.35 REMARK 500 LYS C 171 110.83 -165.84 REMARK 500 PRO C 173 -92.25 -101.89 REMARK 500 PRO C 179 160.47 -41.61 REMARK 500 ASP C 180 -108.25 177.00 REMARK 500 LYS C 182 -74.21 71.00 REMARK 500 ILE C 184 126.04 -175.86 REMARK 500 LYS C 190 -68.69 -125.32 REMARK 500 HIS C 223 -177.87 -171.68 REMARK 500 GLN C 225 67.52 73.14 REMARK 500 PRO X 157 34.22 -78.17 REMARK 500 PRO X 173 -75.76 -56.71 REMARK 500 LYS X 182 -67.35 -135.51 REMARK 500 LYS X 190 -45.54 -138.36 REMARK 500 ASN X 196 75.18 65.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG X 224 0.29 SIDE CHAIN 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 GOL B 1109 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RV6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PLGF IN COMPLEX WITH DOMAIN 2 OF VEGFR1 REMARK 900 RELATED ID: 2C7W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR-B: REMARK 900 IDENTIFICATION OF AMINO ACIDS IMPORTANT FOR ANGIOGENINC ACTIVITY REMARK 900 RELATED ID: 1QSV RELATED DB: PDB REMARK 900 THE VEGF-BINDING DOMAIN OF FLT-1, 20 NMR STRUCTURES REMARK 900 RELATED ID: 2VWE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VASCULAR ENDOTHELIAL GROWTH FACTOR-B IN REMARK 900 COMPLEX WITH A NEUTRALIZING ANTIBODY FAB FRAGMENT REMARK 900 RELATED ID: 1QTY RELATED DB: PDB REMARK 900 VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE REMARK 900 FLT-1 RECEPTOR REMARK 900 RELATED ID: 1QSZ RELATED DB: PDB REMARK 900 THE VEGF-BINDING DOMAIN OF FLT-1 ( MINIMIZED MEAN) REMARK 900 RELATED ID: 1FLT RELATED DB: PDB REMARK 900 VEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT -1 RECEPTOR DBREF 2XAC A 10 108 UNP P49765 VEGFB_HUMAN 31 129 DBREF 2XAC B 10 108 UNP P49765 VEGFB_HUMAN 31 129 DBREF 2XAC C 129 226 UNP P17948 VGFR1_HUMAN 129 226 DBREF 2XAC X 129 226 UNP P17948 VGFR1_HUMAN 129 226 SEQRES 1 A 99 HIS GLN ARG LYS VAL VAL SER TRP ILE ASP VAL TYR THR SEQRES 2 A 99 ARG ALA THR CYS GLN PRO ARG GLU VAL VAL VAL PRO LEU SEQRES 3 A 99 THR VAL GLU LEU MET GLY THR VAL ALA LYS GLN LEU VAL SEQRES 4 A 99 PRO SER CYS VAL THR VAL GLN ARG CYS GLY GLY CYS CYS SEQRES 5 A 99 PRO ASP ASP GLY LEU GLU CYS VAL PRO THR GLY GLN HIS SEQRES 6 A 99 GLN VAL ARG MET GLN ILE LEU MET ILE ARG TYR PRO SER SEQRES 7 A 99 SER GLN LEU GLY GLU MET SER LEU GLU GLU HIS SER GLN SEQRES 8 A 99 CYS GLU CYS ARG PRO LYS LYS LYS SEQRES 1 B 99 HIS GLN ARG LYS VAL VAL SER TRP ILE ASP VAL TYR THR SEQRES 2 B 99 ARG ALA THR CYS GLN PRO ARG GLU VAL VAL VAL PRO LEU SEQRES 3 B 99 THR VAL GLU LEU MET GLY THR VAL ALA LYS GLN LEU VAL SEQRES 4 B 99 PRO SER CYS VAL THR VAL GLN ARG CYS GLY GLY CYS CYS SEQRES 5 B 99 PRO ASP ASP GLY LEU GLU CYS VAL PRO THR GLY GLN HIS SEQRES 6 B 99 GLN VAL ARG MET GLN ILE LEU MET ILE ARG TYR PRO SER SEQRES 7 B 99 SER GLN LEU GLY GLU MET SER LEU GLU GLU HIS SER GLN SEQRES 8 B 99 CYS GLU CYS ARG PRO LYS LYS LYS SEQRES 1 C 98 SER ASP THR GLY ARG PRO PHE VAL GLU MET TYR SER GLU SEQRES 2 C 98 ILE PRO GLU ILE ILE HIS MET THR GLU GLY ARG GLU LEU SEQRES 3 C 98 VAL ILE PRO CYS ARG VAL THR SER PRO ASN ILE THR VAL SEQRES 4 C 98 THR LEU LYS LYS PHE PRO LEU ASP THR LEU ILE PRO ASP SEQRES 5 C 98 GLY LYS ARG ILE ILE TRP ASP SER ARG LYS GLY PHE ILE SEQRES 6 C 98 ILE SER ASN ALA THR TYR LYS GLU ILE GLY LEU LEU THR SEQRES 7 C 98 CYS GLU ALA THR VAL ASN GLY HIS LEU TYR LYS THR ASN SEQRES 8 C 98 TYR LEU THR HIS ARG GLN THR SEQRES 1 X 98 SER ASP THR GLY ARG PRO PHE VAL GLU MET TYR SER GLU SEQRES 2 X 98 ILE PRO GLU ILE ILE HIS MET THR GLU GLY ARG GLU LEU SEQRES 3 X 98 VAL ILE PRO CYS ARG VAL THR SER PRO ASN ILE THR VAL SEQRES 4 X 98 THR LEU LYS LYS PHE PRO LEU ASP THR LEU ILE PRO ASP SEQRES 5 X 98 GLY LYS ARG ILE ILE TRP ASP SER ARG LYS GLY PHE ILE SEQRES 6 X 98 ILE SER ASN ALA THR TYR LYS GLU ILE GLY LEU LEU THR SEQRES 7 X 98 CYS GLU ALA THR VAL ASN GLY HIS LEU TYR LYS THR ASN SEQRES 8 X 98 TYR LEU THR HIS ARG GLN THR HET GOL B1109 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *33(H2 O) HELIX 1 1 ILE A 18 ALA A 24 1 7 HELIX 2 2 SER B 16 ARG B 23 1 8 HELIX 3 3 THR C 198 ILE C 202 5 5 SHEET 1 AA 2 GLN A 27 PRO A 34 0 SHEET 2 AA 2 CYS A 51 GLY A 58 -1 O VAL A 52 N VAL A 33 SHEET 1 AB 3 GLN A 46 VAL A 48 0 SHEET 2 AB 3 LEU A 66 ILE A 83 -1 O LEU A 81 N VAL A 48 SHEET 3 AB 3 GLN A 89 PRO A 105 -1 O GLN A 89 N MET A 82 SHEET 1 BA 2 GLN B 27 PRO B 34 0 SHEET 2 BA 2 CYS B 51 GLY B 58 -1 O VAL B 52 N VAL B 33 SHEET 1 BB 3 LYS B 45 VAL B 48 0 SHEET 2 BB 3 ILE B 80 ARG B 84 -1 O LEU B 81 N VAL B 48 SHEET 3 BB 3 LEU B 90 GLY B 91 -1 O GLY B 91 N ILE B 80 SHEET 1 BC 2 LEU B 66 GLN B 75 0 SHEET 2 BC 2 GLU B 96 PRO B 105 -1 O GLU B 97 N HIS B 74 SHEET 1 CA 4 GLU C 144 HIS C 147 0 SHEET 2 CA 4 HIS C 214 HIS C 223 1 O ASN C 219 N GLU C 144 SHEET 3 CA 4 LEU C 204 VAL C 211 -1 O LEU C 205 N TYR C 220 SHEET 4 CA 4 THR C 168 LEU C 169 -1 O THR C 168 N GLU C 208 SHEET 1 CB 2 LEU C 154 ILE C 156 0 SHEET 2 CB 2 PHE C 192 ILE C 194 -1 O PHE C 192 N ILE C 156 SHEET 1 XA 5 GLU X 144 HIS X 147 0 SHEET 2 XA 5 HIS X 214 HIS X 223 1 O ASN X 219 N GLU X 144 SHEET 3 XA 5 GLY X 203 VAL X 211 -1 O GLY X 203 N THR X 222 SHEET 4 XA 5 THR X 168 LYS X 171 -1 O THR X 168 N GLU X 208 SHEET 5 XA 5 ASP X 175 LEU X 177 -1 O ASP X 175 N LYS X 171 SHEET 1 XB 3 LEU X 154 ILE X 156 0 SHEET 2 XB 3 GLY X 191 ILE X 194 -1 O PHE X 192 N ILE X 156 SHEET 3 XB 3 ILE X 184 ASP X 187 -1 O ILE X 185 N ILE X 193 SSBOND 1 CYS A 26 CYS A 68 1555 1555 2.02 SSBOND 2 CYS A 51 CYS B 60 1555 1555 2.03 SSBOND 3 CYS A 57 CYS A 101 1555 1555 2.03 SSBOND 4 CYS A 60 CYS B 51 1555 1555 2.03 SSBOND 5 CYS A 61 CYS A 103 1555 1555 2.04 SSBOND 6 CYS B 26 CYS B 68 1555 1555 2.03 SSBOND 7 CYS B 57 CYS B 101 1555 1555 2.03 SSBOND 8 CYS B 61 CYS B 103 1555 1555 2.04 SSBOND 9 CYS C 158 CYS C 207 1555 1555 2.04 SSBOND 10 CYS X 158 CYS X 207 1555 1555 2.03 CISPEP 1 VAL A 48 PRO A 49 0 -0.10 CISPEP 2 VAL B 48 PRO B 49 0 -2.05 CISPEP 3 TYR B 85 PRO B 86 0 18.61 CISPEP 4 PHE C 172 PRO C 173 0 16.95 CISPEP 5 PHE X 172 PRO X 173 0 8.37 SITE 1 AC1 7 GLN A 73 HIS A 74 SER A 99 HOH A2009 SITE 2 AC1 7 GLN B 73 HIS B 74 SER B 99 CRYST1 39.212 65.526 82.824 90.00 90.26 90.00 P 1 21 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 0.025502 0.000000 0.000116 0.00000 SCALE2 0.000000 0.015261 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012074 0.00000