PDB Short entry for 1RV6 HEADER HORMONE/GROWTH FACTOR/RECEPTOR 12-DEC-03 1RV6 TITLE CRYSTAL STRUCTURE OF PLGF IN COMPLEX WITH DOMAIN 2 OF VEGFR1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLACENTA GROWTH FACTOR (PLGF); COMPND 3 CHAIN: V, W; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: FLT1 PROTEIN; COMPND 8 CHAIN: X, Y; COMPND 9 FRAGMENT: DOMAIN-2; COMPND 10 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 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PLGF, VEGF FAMILY, CYSTINE KNOT, GROWTH FACTOR, LIGAND-RECEPTOR KEYWDS 2 COMPLEX, SPECIFICITY, HORMONE-GROWTH FACTOR-RECEPTOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.W.CHRISTINGER,G.FUH,A.M.DE VOS,C.WIESMANN REVDAT 5 23-AUG-23 1RV6 1 REMARK REVDAT 4 13-JUL-11 1RV6 1 VERSN REVDAT 3 24-FEB-09 1RV6 1 VERSN REVDAT 2 20-APR-04 1RV6 1 JRNL REMARK MASTER REVDAT 1 20-JAN-04 1RV6 0 JRNL AUTH H.W.CHRISTINGER,G.FUH,A.M.DE VOS,C.WIESMANN JRNL TITL THE CRYSTAL STRUCTURE OF PLACENTAL GROWTH FACTOR IN COMPLEX JRNL TITL 2 WITH DOMAIN 2 OF VASCULAR ENDOTHELIAL GROWTH FACTOR JRNL TITL 3 RECEPTOR-1. JRNL REF J.BIOL.CHEM. V. 279 10382 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 14684734 JRNL DOI 10.1074/JBC.M313237200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.WIESMANN,G.FUH,C.H.CHRISTINGER,C.EIGENBROT,J.A.WELLS, REMARK 1 AUTH 2 A.M.DE VOS REMARK 1 TITL CRYSTAL STRUCTURE AT 1.7 A RESOLUTION OF VEGF IN COMPLEX REMARK 1 TITL 2 WITH DOMAIN 2 OF THE FLT-1 RECEPTOR REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 91 695 1997 REMARK 1 REFN ISSN 0092-8674 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.IYER,D.DEMETRES,G.LEONIDAS,J.SWAMINATHAN,D.MAGLIONE, REMARK 1 AUTH 2 M.BATTISTI,M.TUCCI,G.PERSICO,K.R.ACHARYA REMARK 1 TITL THE CRYSTAL STRUCTURE OF HUMAN PLACENTA GROWTH FACTOR-1 REMARK 1 TITL 2 (PLGF-1), AN ANGIOGENIC PROTEIN, AT 2.0 A RESOLUTION. REMARK 1 REF J.BIOL.CHEM. V. 276 12153 2001 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M008055200 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.07 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15482 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1153 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 25 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.50 REMARK 3 REFLECTION IN BIN (WORKING SET) : 845 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2985 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 161 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.78000 REMARK 3 B22 (A**2) : -0.95000 REMARK 3 B33 (A**2) : 1.74000 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): 0.514 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.295 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.198 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.654 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3078 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4184 ; 1.556 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 369 ; 6.686 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;36.168 ;22.632 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 533 ;18.714 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;17.083 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 479 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2272 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1185 ; 0.216 ; 0.200 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): 180 ; 0.152 ; 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): 56 ; 0.173 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.147 ; 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): 1867 ; 3.008 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3070 ; 4.649 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1211 ; 3.749 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1114 ; 5.405 ; 5.000 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 : 4 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 : V 22 V 115 REMARK 3 ORIGIN FOR THE GROUP (A): 7.6291 32.8255 17.8849 REMARK 3 T TENSOR REMARK 3 T11: 0.0783 T22: 0.0634 REMARK 3 T33: 0.0164 T12: 0.0192 REMARK 3 T13: -0.0214 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 9.0822 L22: 1.4092 REMARK 3 L33: 0.9021 L12: 0.9677 REMARK 3 L13: -0.8503 L23: 0.2559 REMARK 3 S TENSOR REMARK 3 S11: 0.1207 S12: -0.3853 S13: 0.3049 REMARK 3 S21: 0.1251 S22: -0.1515 S23: 0.0790 REMARK 3 S31: -0.0687 S32: -0.0004 S33: 0.0307 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 : W 21 W 115 REMARK 3 ORIGIN FOR THE GROUP (A): 22.2917 23.7364 19.5114 REMARK 3 T TENSOR REMARK 3 T11: 0.1014 T22: 0.0954 REMARK 3 T33: 0.0718 T12: 0.0112 REMARK 3 T13: -0.0073 T23: 0.0320 REMARK 3 L TENSOR REMARK 3 L11: 8.7291 L22: 1.1355 REMARK 3 L33: 0.0643 L12: 2.8452 REMARK 3 L13: 0.4275 L23: 0.4534 REMARK 3 S TENSOR REMARK 3 S11: 0.1476 S12: -0.3190 S13: -0.1455 REMARK 3 S21: 0.1205 S22: -0.1544 S23: -0.0760 REMARK 3 S31: 0.0932 S32: 0.0069 S33: 0.0068 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 : X 133 X 224 REMARK 3 ORIGIN FOR THE GROUP (A): -4.9886 3.5484 12.7052 REMARK 3 T TENSOR REMARK 3 T11: 0.2635 T22: 0.0749 REMARK 3 T33: 0.1206 T12: -0.0617 REMARK 3 T13: -0.0470 T23: 0.0424 REMARK 3 L TENSOR REMARK 3 L11: 3.6224 L22: 2.5549 REMARK 3 L33: 9.7249 L12: 0.6880 REMARK 3 L13: -0.1172 L23: 0.8763 REMARK 3 S TENSOR REMARK 3 S11: 0.0370 S12: -0.0812 S13: -0.2924 REMARK 3 S21: 0.0736 S22: 0.0897 S23: 0.1166 REMARK 3 S31: 0.7811 S32: -0.4831 S33: -0.1267 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : Y 133 Y 224 REMARK 3 ORIGIN FOR THE GROUP (A): 35.5832 49.7000 5.8560 REMARK 3 T TENSOR REMARK 3 T11: 0.3252 T22: 0.1622 REMARK 3 T33: 0.4911 T12: -0.0351 REMARK 3 T13: 0.1198 T23: 0.1021 REMARK 3 L TENSOR REMARK 3 L11: 11.0444 L22: 6.2688 REMARK 3 L33: 10.5123 L12: 0.0652 REMARK 3 L13: -3.9352 L23: -2.2192 REMARK 3 S TENSOR REMARK 3 S11: 0.5986 S12: 0.4017 S13: 1.3665 REMARK 3 S21: -0.3208 S22: -0.0489 S23: -0.6714 REMARK 3 S31: -0.7068 S32: 0.2567 S33: -0.5497 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 1RV6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000021062. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15482 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.16100 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1FLT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 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 27.14050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.67300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.98950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.67300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.14050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.98950 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: V, W, X, Y 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 GLU V 19 REMARK 465 VAL V 20 REMARK 465 GLU V 21 REMARK 465 ARG V 116 REMARK 465 GLU V 117 REMARK 465 LYS V 118 REMARK 465 MET V 119 REMARK 465 GLU W 19 REMARK 465 VAL W 20 REMARK 465 ARG W 116 REMARK 465 GLU W 117 REMARK 465 LYS W 118 REMARK 465 MET W 119 REMARK 465 ASP X 130 REMARK 465 THR X 131 REMARK 465 GLY X 132 REMARK 465 GLN X 225 REMARK 465 THR X 226 REMARK 465 ASN X 227 REMARK 465 THR X 228 REMARK 465 ILE X 229 REMARK 465 ASP Y 130 REMARK 465 THR Y 131 REMARK 465 GLY Y 132 REMARK 465 GLN Y 225 REMARK 465 THR Y 226 REMARK 465 ASN Y 227 REMARK 465 THR Y 228 REMARK 465 ILE Y 229 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 OE2 GLU W 27 NH1 ARG W 31 2.15 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 LEU V 88 CA - CB - CG ANGL. DEV. = 16.7 DEGREES REMARK 500 LEU W 88 CA - CB - CG ANGL. DEV. = 14.4 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 CYS V 34 107.08 -166.12 REMARK 500 ARG V 96 154.34 140.46 REMARK 500 CYS W 34 107.77 -173.16 REMARK 500 GLU X 141 -78.73 -94.81 REMARK 500 GLU X 150 119.57 -34.57 REMARK 500 PRO X 157 33.87 -77.56 REMARK 500 LYS X 182 -57.19 -128.94 REMARK 500 PRO Y 157 34.76 -76.08 REMARK 500 ASN Y 164 45.79 -89.80 REMARK 500 LYS Y 182 -36.93 -152.16 REMARK 500 ASN Y 196 85.87 66.70 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 B3P W 301 DBREF 1RV6 V 19 119 UNP P49763 PLGF_HUMAN 37 131 DBREF 1RV6 W 19 119 UNP P49763 PLGF_HUMAN 37 131 DBREF 1RV6 X 130 229 UNP P17948 VGFR1_HUMAN 130 229 DBREF 1RV6 Y 130 229 UNP P17948 VGFR1_HUMAN 130 229 SEQRES 1 V 101 GLU VAL GLU VAL VAL PRO PHE GLN GLU VAL TRP GLY ARG SEQRES 2 V 101 SER TYR CYS ARG ALA LEU GLU ARG LEU VAL ASP VAL VAL SEQRES 3 V 101 SER GLU TYR PRO SER GLU VAL GLU HIS MET PHE SER PRO SEQRES 4 V 101 SER CYS VAL SER LEU LEU ARG CYS THR GLY CYS CYS GLY SEQRES 5 V 101 ASP GLU ASN LEU HIS CYS VAL PRO VAL GLU THR ALA ASN SEQRES 6 V 101 VAL THR MET GLN LEU LEU LYS ILE ARG SER GLY ASP ARG SEQRES 7 V 101 PRO SER TYR VAL GLU LEU THR PHE SER GLN HIS VAL ARG SEQRES 8 V 101 CYS GLU CYS ARG PRO LEU ARG GLU LYS MET SEQRES 1 W 101 GLU VAL GLU VAL VAL PRO PHE GLN GLU VAL TRP GLY ARG SEQRES 2 W 101 SER TYR CYS ARG ALA LEU GLU ARG LEU VAL ASP VAL VAL SEQRES 3 W 101 SER GLU TYR PRO SER GLU VAL GLU HIS MET PHE SER PRO SEQRES 4 W 101 SER CYS VAL SER LEU LEU ARG CYS THR GLY CYS CYS GLY SEQRES 5 W 101 ASP GLU ASN LEU HIS CYS VAL PRO VAL GLU THR ALA ASN SEQRES 6 W 101 VAL THR MET GLN LEU LEU LYS ILE ARG SER GLY ASP ARG SEQRES 7 W 101 PRO SER TYR VAL GLU LEU THR PHE SER GLN HIS VAL ARG SEQRES 8 W 101 CYS GLU CYS ARG PRO LEU ARG GLU LYS MET SEQRES 1 X 100 ASP THR GLY ARG PRO PHE VAL GLU MET TYR SER GLU ILE SEQRES 2 X 100 PRO GLU ILE ILE HIS MET THR GLU GLY ARG GLU LEU VAL SEQRES 3 X 100 ILE PRO CYS ARG VAL THR SER PRO ASN ILE THR VAL THR SEQRES 4 X 100 LEU LYS LYS PHE PRO LEU ASP THR LEU ILE PRO ASP GLY SEQRES 5 X 100 LYS ARG ILE ILE TRP ASP SER ARG LYS GLY PHE ILE ILE SEQRES 6 X 100 SER ASN ALA THR TYR LYS GLU ILE GLY LEU LEU THR CYS SEQRES 7 X 100 GLU ALA THR VAL ASN GLY HIS LEU TYR LYS THR ASN TYR SEQRES 8 X 100 LEU THR HIS ARG GLN THR ASN THR ILE SEQRES 1 Y 100 ASP THR GLY ARG PRO PHE VAL GLU MET TYR SER GLU ILE SEQRES 2 Y 100 PRO GLU ILE ILE HIS MET THR GLU GLY ARG GLU LEU VAL SEQRES 3 Y 100 ILE PRO CYS ARG VAL THR SER PRO ASN ILE THR VAL THR SEQRES 4 Y 100 LEU LYS LYS PHE PRO LEU ASP THR LEU ILE PRO ASP GLY SEQRES 5 Y 100 LYS ARG ILE ILE TRP ASP SER ARG LYS GLY PHE ILE ILE SEQRES 6 Y 100 SER ASN ALA THR TYR LYS GLU ILE GLY LEU LEU THR CYS SEQRES 7 Y 100 GLU ALA THR VAL ASN GLY HIS LEU TYR LYS THR ASN TYR SEQRES 8 Y 100 LEU THR HIS ARG GLN THR ASN THR ILE HET B3P W 301 19 HETNAM B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)- HETNAM 2 B3P PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL FORMUL 5 B3P C11 H26 N2 O6 FORMUL 6 HOH *161(H2 O) HELIX 1 1 PRO V 24 TYR V 33 1 10 HELIX 2 2 VAL V 43 TYR V 47 1 5 HELIX 3 3 PRO W 24 TYR W 33 1 10 HELIX 4 4 VAL W 43 TYR W 47 1 5 HELIX 5 5 PRO W 48 VAL W 51 5 4 HELIX 6 6 THR X 198 ILE X 202 5 5 HELIX 7 7 THR Y 198 ILE Y 202 5 5 SHEET 1 A 2 ARG V 35 ASP V 42 0 SHEET 2 A 2 CYS V 59 THR V 66 -1 O ARG V 64 N LEU V 37 SHEET 1 B 3 MET V 54 SER V 56 0 SHEET 2 B 3 LEU V 74 ILE V 91 -1 O LEU V 89 N SER V 56 SHEET 3 B 3 SER V 98 PRO V 114 -1 O GLN V 106 N ALA V 82 SHEET 1 C 2 ARG W 35 ASP W 42 0 SHEET 2 C 2 CYS W 59 THR W 66 -1 O VAL W 60 N VAL W 41 SHEET 1 D 3 MET W 54 SER W 56 0 SHEET 2 D 3 LEU W 74 ILE W 91 -1 O ILE W 91 N MET W 54 SHEET 3 D 3 SER W 98 PRO W 114 -1 O GLN W 106 N ALA W 82 SHEET 1 E 5 GLU X 144 HIS X 147 0 SHEET 2 E 5 HIS X 214 HIS X 223 1 O LEU X 221 N GLU X 144 SHEET 3 E 5 GLY X 203 VAL X 211 -1 N LEU X 205 O TYR X 220 SHEET 4 E 5 THR X 168 LYS X 171 -1 N LYS X 170 O THR X 206 SHEET 5 E 5 ASP X 175 LEU X 177 -1 O LEU X 177 N LEU X 169 SHEET 1 F 3 LEU X 154 ILE X 156 0 SHEET 2 F 3 GLY X 191 ILE X 194 -1 O ILE X 194 N LEU X 154 SHEET 3 F 3 ILE X 184 ASP X 187 -1 N ILE X 185 O ILE X 193 SHEET 1 G 5 GLU Y 144 HIS Y 147 0 SHEET 2 G 5 LEU Y 215 HIS Y 223 1 O LEU Y 221 N ILE Y 146 SHEET 3 G 5 LEU Y 204 THR Y 210 -1 N ALA Y 209 O TYR Y 216 SHEET 4 G 5 THR Y 168 LYS Y 171 -1 N LYS Y 170 O THR Y 206 SHEET 5 G 5 ASP Y 175 LEU Y 177 -1 O ASP Y 175 N LYS Y 171 SHEET 1 H 3 LEU Y 154 ILE Y 156 0 SHEET 2 H 3 GLY Y 191 ILE Y 194 -1 O ILE Y 194 N LEU Y 154 SHEET 3 H 3 ILE Y 184 ASP Y 187 -1 N ASP Y 187 O GLY Y 191 SSBOND 1 CYS V 34 CYS V 76 1555 1555 2.05 SSBOND 2 CYS V 59 CYS W 68 1555 1555 2.08 SSBOND 3 CYS V 65 CYS V 110 1555 1555 2.03 SSBOND 4 CYS V 68 CYS W 59 1555 1555 2.06 SSBOND 5 CYS V 69 CYS V 112 1555 1555 2.04 SSBOND 6 CYS W 34 CYS W 76 1555 1555 2.03 SSBOND 7 CYS W 65 CYS W 110 1555 1555 2.04 SSBOND 8 CYS W 69 CYS W 112 1555 1555 2.07 SSBOND 9 CYS X 158 CYS X 207 1555 1555 2.02 SSBOND 10 CYS Y 158 CYS Y 207 1555 1555 2.06 CISPEP 1 SER V 56 PRO V 57 0 1.41 CISPEP 2 SER W 56 PRO W 57 0 3.73 CISPEP 3 PHE X 172 PRO X 173 0 2.47 CISPEP 4 PHE Y 172 PRO Y 173 0 -1.01 SITE 1 AC1 9 GLN V 87 TYR V 99 GLU V 101 GLN W 87 SITE 2 AC1 9 TYR W 99 GLU W 101 HOH W 323 GLU X 141 SITE 3 AC1 9 GLU Y 141 CRYST1 54.281 71.979 115.346 90.00 90.00 90.00 P 21 21 21 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 0.018423 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013893 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008670 0.00000