HEADER CELL CYCLE, HORMONE/GROWTH FACTOR 02-NOV-01 1KAT TITLE SOLUTION STRUCTURE OF A PHAGE-DERIVED PEPTIDE ANTAGONIST IN COMPLEX TITLE 2 WITH VASCULAR ENDOTHELIAL GROWTH FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR; COMPND 3 CHAIN: V, W; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN; COMPND 5 SYNONYM: VEGF; VASCULAR PERMEABILITY FACTOR; VPF; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PHAGE-DERIVED PEPTIDE ANTAGONIST; COMPND 9 CHAIN: X, Y; COMPND 10 SYNONYM: V107; COMPND 11 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: VEGF OR VEGFA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES KEYWDS PROTEIN-PEPTIDE COMPLEX, HOMODIMER, CYSTINE KNOT, CELL CYCLE, KEYWDS 2 HORMONE-GROWTH FACTOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 24 AUTHOR B.PAN,B.LI,S.J.RUSSELL,J.Y.K.TOM,A.G.COCHRAN,W.J.FAIRBROTHER REVDAT 5 20-NOV-24 1KAT 1 REMARK REVDAT 4 23-FEB-22 1KAT 1 REMARK REVDAT 3 24-FEB-09 1KAT 1 VERSN REVDAT 2 30-SEP-03 1KAT 1 DBREF REVDAT 1 02-NOV-02 1KAT 0 JRNL AUTH B.PAN,B.LI,S.J.RUSSELL,J.Y.K.TOM,A.G.COCHRAN,W.J.FAIRBROTHER JRNL TITL SOLUTION STRUCTURE OF A PHAGE-DERIVED PEPTIDE ANTAGONIST IN JRNL TITL 2 COMPLEX WITH VASCULAR ENDOTHELIAL GROWTH FACTOR JRNL REF J.MOL.BIOL. V. 316 769 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 11866530 JRNL DOI 10.1006/JMBI.2001.5370 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CNX 2000.1 REMARK 3 AUTHORS : BRUKER, INC. (XWINNMR), ACCELYS, INC. (CNX) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 3940 NOE REMARK 3 -DERIVED DISTANCE RESTRAINTS, 176 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN BONDS, 476 DIHEDRAL ANGLE RESTRAINTS, 146 RESIDUAL REMARK 3 DIPOLAR COUPLING RESTRAINTS. REMARK 4 REMARK 4 1KAT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014765. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 318; 298 REMARK 210 PH : 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 50MM SODIUM CHLORIDE, 20 SODIUM REMARK 210 PHOSPHATE; 50MM SODIUM CHLORIDE, REMARK 210 20 SODIUM PHOSPHATE; 50MM SODIUM REMARK 210 CHLORIDE, 20 SODIUM PHOSPHATE REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.6MM U-13C/15N LABELED V107 + REMARK 210 0.45 MM UNLABELED VEGF DIMER; REMARK 210 50MM SODIUM CHLORIDE, 20MM REMARK 210 PHOSPHATE BUFFER, 0.002% SODIUM REMARK 210 AZIDE; 0.6MM U-13C/15N LABELED REMARK 210 V107 + 0.45 MM UNLABELED VEGF REMARK 210 DIMER; 50MM SODIUM CHLORIDE, REMARK 210 20MM PHOSPHATE BUFFER, 0.002% REMARK 210 SODIUM AZIDE; 1.0MM U-13C/15N REMARK 210 LABELED VEGF DIMER + 2.25 MM REMARK 210 UNLABELED V107; 50MM SODIUM REMARK 210 CHLORIDE, 20MM PHOSPHATE BUFFER, REMARK 210 0.002% SODIUM AZIDE; 1.0MM U-13C/ REMARK 210 15N LABELED VEGF DIMER + 2.25 MM REMARK 210 UNLABELED V107; 50MM SODIUM REMARK 210 CHLORIDE, 20MM PHOSPHATE BUFFER, REMARK 210 0.002% SODIUM AZIDE; 0.6MM U-13C/ REMARK 210 15N LABELED V107 + 0.45 MM REMARK 210 UNLABELED VEGF DIMER; 50MM REMARK 210 SODIUM CHLORIDE, 20MM PHOSPHATE REMARK 210 BUFFER, 0.002% SODIUM AZIDE, REMARK 210 15MG/ML PF1 PHAGE; 1.0MM U-13C/ REMARK 210 15N LABELED VEGF DIMER + 2.25 MM REMARK 210 UNLABELED V107; 50MM SODIUM REMARK 210 CHLORIDE, 20MM PHOSPHATE BUFFER, REMARK 210 0.002% SODIUM AZIDE, 15MG/ML PF1 REMARK 210 PHAGE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; IPAP_1H_15N_HSQC; 3D_13C-EDITED_12C-FILTERED_ REMARK 210 NOESY; 3D_12C-FILTERED_13C-EDITED_NOESY; HNHB; HMSQC-HA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 98.0, XEASY 1.3.13, CNX REMARK 210 2000.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 120 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 24 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 9 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 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 1 HIS V 12 -83.42 -86.12 REMARK 500 1 GLU V 13 179.80 172.69 REMARK 500 1 CYS V 26 103.25 -39.91 REMARK 500 1 GLN V 87 -124.52 -120.21 REMARK 500 1 GLU W 13 -174.28 65.78 REMARK 500 1 CYS W 26 102.66 -38.50 REMARK 500 1 GLN W 87 -122.81 -120.97 REMARK 500 1 HIS W 90 149.40 -171.67 REMARK 500 1 LYS W 108 -70.57 -110.74 REMARK 500 1 ASN X 3 47.95 -157.08 REMARK 500 1 GLU X 4 40.32 -99.66 REMARK 500 1 ALA X 8 33.37 -97.93 REMARK 500 1 MET X 10 96.54 -54.69 REMARK 500 1 TRP X 11 92.79 -68.05 REMARK 500 1 GLU X 12 -172.72 -60.13 REMARK 500 1 ARG X 18 70.95 -117.49 REMARK 500 1 ASN Y 3 40.60 -164.06 REMARK 500 1 GLU Y 4 46.42 -97.73 REMARK 500 1 ALA Y 8 33.01 -98.67 REMARK 500 1 MET Y 10 95.23 -51.60 REMARK 500 1 TRP Y 11 94.18 -66.14 REMARK 500 1 GLU Y 12 -172.04 -61.26 REMARK 500 1 ARG Y 18 68.81 -111.45 REMARK 500 2 GLU V 13 21.20 -148.12 REMARK 500 2 CYS V 26 100.80 -37.22 REMARK 500 2 TYR V 39 74.98 -114.41 REMARK 500 2 HIS V 86 -2.44 75.12 REMARK 500 2 GLN V 87 -116.19 -123.16 REMARK 500 2 LYS V 108 -64.18 -137.67 REMARK 500 2 CYS W 26 101.90 -39.08 REMARK 500 2 TYR W 39 75.99 -114.60 REMARK 500 2 HIS W 86 -2.24 74.96 REMARK 500 2 GLN W 87 -118.56 -122.63 REMARK 500 2 LYS W 108 40.48 -162.98 REMARK 500 2 ALA X 8 36.38 -99.80 REMARK 500 2 MET X 10 95.02 -50.03 REMARK 500 2 TRP X 11 88.32 -69.59 REMARK 500 2 GLU X 12 -174.89 -57.20 REMARK 500 2 ASN Y 3 84.69 -62.20 REMARK 500 2 MET Y 10 95.07 -48.82 REMARK 500 2 TRP Y 11 90.42 -69.81 REMARK 500 2 GLU Y 12 -173.57 -59.30 REMARK 500 3 HIS V 12 84.82 -176.64 REMARK 500 3 GLU V 13 -76.54 -66.47 REMARK 500 3 CYS V 26 104.75 -38.18 REMARK 500 3 TYR V 39 77.21 -118.98 REMARK 500 3 PRO V 85 104.23 -58.18 REMARK 500 3 HIS W 12 -42.57 -170.25 REMARK 500 3 GLU W 13 -88.22 60.61 REMARK 500 3 CYS W 26 103.94 -39.61 REMARK 500 REMARK 500 THIS ENTRY HAS 404 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5185 RELATED DB: BMRB REMARK 900 1H, 13C, AND 15N RESONANCE ASSIGNMENT OF THE VASCULAR ENDOTHELIAL REMARK 900 GROWTH FACTOR RECEPTOR-BINDING DOMAIN IN COMPLEX WITH A RECEPTOR- REMARK 900 BLOCKING PEPTIDE. REMARK 900 RELATED ID: 5198 RELATED DB: BMRB REMARK 900 1H, 13C, AND 15N RESONANCE ASSIGNMENT OF A RECEPTOR-BLOCKING REMARK 900 PEPTIDE IN COMPLEX WITH THE VASCULAR ENDOTHELIAL GROWTH FACTOR REMARK 900 RECEPTOR-BINDING DOMAIN. DBREF 1KAT V 11 109 UNP P15692 VEGFA_HUMAN 37 135 DBREF 1KAT W 11 109 UNP P15692 VEGFA_HUMAN 37 135 DBREF 1KAT X 1 19 PDB 1KAT 1KAT 1 19 DBREF 1KAT Y 1 19 PDB 1KAT 1KAT 1 19 SEQRES 1 V 99 HIS HIS GLU VAL VAL LYS PHE MET ASP VAL TYR GLN ARG SEQRES 2 V 99 SER TYR CYS HIS PRO ILE GLU THR LEU VAL ASP ILE PHE SEQRES 3 V 99 GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE PHE LYS PRO SEQRES 4 V 99 SER CYS VAL PRO LEU MET ARG CYS GLY GLY CYS CYS ASN SEQRES 5 V 99 ASP GLU GLY LEU GLU CYS VAL PRO THR GLU GLU SER ASN SEQRES 6 V 99 ILE THR MET GLN ILE MET ARG ILE LYS PRO HIS GLN GLY SEQRES 7 V 99 GLN HIS ILE GLY GLU MET SER PHE LEU GLN HIS ASN LYS SEQRES 8 V 99 CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 W 99 HIS HIS GLU VAL VAL LYS PHE MET ASP VAL TYR GLN ARG SEQRES 2 W 99 SER TYR CYS HIS PRO ILE GLU THR LEU VAL ASP ILE PHE SEQRES 3 W 99 GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE PHE LYS PRO SEQRES 4 W 99 SER CYS VAL PRO LEU MET ARG CYS GLY GLY CYS CYS ASN SEQRES 5 W 99 ASP GLU GLY LEU GLU CYS VAL PRO THR GLU GLU SER ASN SEQRES 6 W 99 ILE THR MET GLN ILE MET ARG ILE LYS PRO HIS GLN GLY SEQRES 7 W 99 GLN HIS ILE GLY GLU MET SER PHE LEU GLN HIS ASN LYS SEQRES 8 W 99 CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 X 19 GLY GLY ASN GLU CYS ASP ILE ALA ARG MET TRP GLU TRP SEQRES 2 X 19 GLU CYS PHE GLU ARG LEU SEQRES 1 Y 19 GLY GLY ASN GLU CYS ASP ILE ALA ARG MET TRP GLU TRP SEQRES 2 Y 19 GLU CYS PHE GLU ARG LEU HELIX 1 1 LYS V 16 TYR V 25 1 10 HELIX 2 2 ILE V 35 TYR V 39 1 5 HELIX 3 3 LYS W 16 TYR W 25 1 10 HELIX 4 4 ILE W 35 TYR W 39 1 5 HELIX 5 5 GLU X 12 ARG X 18 1 7 HELIX 6 6 GLU Y 12 ARG Y 18 1 7 SHEET 1 A 2 HIS V 27 ASP V 34 0 SHEET 2 A 2 CYS V 51 GLY V 58 -1 O ARG V 56 N ILE V 29 SHEET 1 B 3 ILE V 46 LYS V 48 0 SHEET 2 B 3 GLU V 73 ILE V 83 -1 O ILE V 83 N ILE V 46 SHEET 3 B 3 GLN V 89 HIS V 99 -1 O GLY V 92 N ILE V 80 SHEET 1 C 2 LEU V 66 PRO V 70 0 SHEET 2 C 2 CYS V 102 PRO V 106 -1 O GLU V 103 N VAL V 69 SHEET 1 D 2 HIS W 27 ASP W 34 0 SHEET 2 D 2 CYS W 51 GLY W 58 -1 O ARG W 56 N ILE W 29 SHEET 1 E 3 ILE W 46 LYS W 48 0 SHEET 2 E 3 GLU W 73 ILE W 83 -1 O ILE W 83 N ILE W 46 SHEET 3 E 3 GLN W 89 HIS W 99 -1 O GLY W 92 N ILE W 80 SHEET 1 F 2 LEU W 66 PRO W 70 0 SHEET 2 F 2 CYS W 102 PRO W 106 -1 O GLU W 103 N VAL W 69 SSBOND 1 CYS V 26 CYS V 68 1555 1555 2.03 SSBOND 2 CYS V 51 CYS W 60 1555 1555 2.03 SSBOND 3 CYS V 57 CYS V 102 1555 1555 2.03 SSBOND 4 CYS V 60 CYS W 51 1555 1555 2.03 SSBOND 5 CYS V 61 CYS V 104 1555 1555 2.03 SSBOND 6 CYS W 26 CYS W 68 1555 1555 2.03 SSBOND 7 CYS W 57 CYS W 102 1555 1555 2.03 SSBOND 8 CYS W 61 CYS W 104 1555 1555 2.03 SSBOND 9 CYS X 5 CYS X 15 1555 1555 2.03 SSBOND 10 CYS Y 5 CYS Y 15 1555 1555 2.03 CISPEP 1 LYS V 48 PRO V 49 1 0.42 CISPEP 2 LYS W 48 PRO W 49 1 0.43 CISPEP 3 LYS V 48 PRO V 49 2 0.55 CISPEP 4 LYS W 48 PRO W 49 2 0.22 CISPEP 5 LYS V 48 PRO V 49 3 0.57 CISPEP 6 LYS W 48 PRO W 49 3 0.67 CISPEP 7 LYS V 48 PRO V 49 4 0.16 CISPEP 8 LYS W 48 PRO W 49 4 0.27 CISPEP 9 LYS V 48 PRO V 49 5 0.49 CISPEP 10 LYS W 48 PRO W 49 5 0.45 CISPEP 11 LYS V 48 PRO V 49 6 0.43 CISPEP 12 LYS W 48 PRO W 49 6 0.44 CISPEP 13 LYS V 48 PRO V 49 7 0.73 CISPEP 14 LYS W 48 PRO W 49 7 0.53 CISPEP 15 LYS V 48 PRO V 49 8 0.36 CISPEP 16 LYS W 48 PRO W 49 8 0.39 CISPEP 17 LYS V 48 PRO V 49 9 0.45 CISPEP 18 LYS W 48 PRO W 49 9 0.57 CISPEP 19 LYS V 48 PRO V 49 10 0.46 CISPEP 20 LYS W 48 PRO W 49 10 0.29 CISPEP 21 LYS V 48 PRO V 49 11 0.63 CISPEP 22 LYS W 48 PRO W 49 11 0.49 CISPEP 23 LYS V 48 PRO V 49 12 0.78 CISPEP 24 LYS W 48 PRO W 49 12 0.65 CISPEP 25 LYS V 48 PRO V 49 13 0.74 CISPEP 26 LYS W 48 PRO W 49 13 0.63 CISPEP 27 LYS V 48 PRO V 49 14 0.47 CISPEP 28 LYS W 48 PRO W 49 14 0.48 CISPEP 29 LYS V 48 PRO V 49 15 0.75 CISPEP 30 LYS W 48 PRO W 49 15 0.56 CISPEP 31 LYS V 48 PRO V 49 16 0.45 CISPEP 32 LYS W 48 PRO W 49 16 0.64 CISPEP 33 LYS V 48 PRO V 49 17 0.72 CISPEP 34 LYS W 48 PRO W 49 17 0.78 CISPEP 35 LYS V 48 PRO V 49 18 0.46 CISPEP 36 LYS W 48 PRO W 49 18 0.68 CISPEP 37 LYS V 48 PRO V 49 19 0.22 CISPEP 38 LYS W 48 PRO W 49 19 0.34 CISPEP 39 LYS V 48 PRO V 49 20 0.96 CISPEP 40 LYS W 48 PRO W 49 20 1.06 CISPEP 41 LYS V 48 PRO V 49 21 0.54 CISPEP 42 LYS W 48 PRO W 49 21 0.41 CISPEP 43 LYS V 48 PRO V 49 22 0.66 CISPEP 44 LYS W 48 PRO W 49 22 0.34 CISPEP 45 LYS V 48 PRO V 49 23 0.43 CISPEP 46 LYS W 48 PRO W 49 23 0.33 CISPEP 47 LYS V 48 PRO V 49 24 0.74 CISPEP 48 LYS W 48 PRO W 49 24 0.66 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1