Header list of 1kat.pdb file
Complete list - b 23 2 Bytes
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 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
Complete list - b 23 2 Bytes