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- PDB-1kat: Solution Structure of a Phage-Derived Peptide Antagonist in Compl... -

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Basic information

Entry
Database: PDB / ID: 1kat
TitleSolution Structure of a Phage-Derived Peptide Antagonist in Complex with Vascular Endothelial Growth Factor
Components
  • Phage-Derived Peptide Antagonist
  • Vascular Endothelial Growth Factor
KeywordsCELL CYCLE / HORMONE/GROWTH FACTOR / Protein-peptide complex / homodimer / cystine knot / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier ...basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / negative regulation of blood-brain barrier permeability / VEGF-activated neuropilin signaling pathway / bone trabecula formation / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / lung vasculature development / lymphangiogenesis / eye photoreceptor cell development / endothelial cell chemotaxis / motor neuron migration / positive regulation of trophoblast cell migration / positive regulation of epithelial tube formation / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization / regulation of nitric oxide mediated signal transduction / positive regulation of axon extension involved in axon guidance / vascular wound healing / positive regulation of protein localization to early endosome / regulation of hematopoietic progenitor cell differentiation / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of branching involved in ureteric bud morphogenesis / camera-type eye morphogenesis / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / vascular endothelial growth factor receptor 2 binding / tube formation / positive regulation of vascular permeability / dopaminergic neuron differentiation / commissural neuron axon guidance / negative regulation of epithelial to mesenchymal transition / platelet-derived growth factor receptor binding / surfactant homeostasis / extracellular matrix binding / cell migration involved in sprouting angiogenesis / cardiac muscle cell development / epithelial cell maturation / sprouting angiogenesis / positive regulation of positive chemotaxis / endothelial cell proliferation / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of leukocyte migration / vascular endothelial growth factor signaling pathway / positive regulation of p38MAPK cascade / positive regulation of endothelial cell chemotaxis / artery morphogenesis / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / retinal ganglion cell axon guidance / positive regulation of neuroblast proliferation / positive chemotaxis / negative regulation of fat cell differentiation / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / chemoattractant activity / outflow tract morphogenesis / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / fibronectin binding / positive regulation of cell division / positive regulation of cell adhesion / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / mammary gland alveolus development / vasculogenesis / positive regulation of osteoblast differentiation / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / ovarian follicle development / cell maturation / homeostasis of number of cells within a tissue / positive regulation of protein autophosphorylation / positive regulation of endothelial cell proliferation / epithelial cell differentiation / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors
Similarity search - Function
Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Cystine Knot Cytokines, subunit B ...Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Torsion angle dynamics simulated annealing
AuthorsPan, B. / Li, B. / Russell, S.J. / Tom, J.Y.K. / Cochran, A.G. / Fairbrother, W.J.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Solution Structure of a Phage-derived Peptide Antagonist in Complex with Vascular Endothelial Growth Factor
Authors: Pan, B. / Li, B. / Russell, S.J. / Tom, J.Y.K. / Cochran, A.G. / Fairbrother, W.J.
History
DepositionNov 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: Vascular Endothelial Growth Factor
W: Vascular Endothelial Growth Factor
X: Phage-Derived Peptide Antagonist
Y: Phage-Derived Peptide Antagonist


Theoretical massNumber of molelcules
Total (without water)27,9924
Polymers27,9924
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 120structures with the least restraint violations
RepresentativeModel #9closest to the average

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Components

#1: Protein Vascular Endothelial Growth Factor / VEGF / VASCULAR PERMEABILITY FACTOR / VPF


Mass: 11649.396 Da / Num. of mol.: 2 / Fragment: Receptor Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VEGF or VEGFA / Production host: Escherichia coli (E. coli) / References: UniProt: P15692
#2: Protein/peptide Phage-Derived Peptide Antagonist / v107


Mass: 2346.620 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
3113D 15N-separated NOESY
1223D 13C-separated NOESY
2333D 15N-separated NOESY
2443D 13C-separated NOESY
255IPAP 1H 15N HSQC
266IPAP 1H 15N HSQC
1723D 13C-edited 12C-filtered NOESY
2843D 12C-filtered 13C-edited NOESY
293HNHB
1101HMSQC-HA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM U-13C/15N labeled v107 + 0.45 mM unlabeled VEGF Dimer; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide90% H2O/10% D2O
20.6mM U-13C/15N labeled v107 + 0.45 mM unlabeled VEGF Dimer; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide100% D2O
31.0mM U-13C/15N labeled VEGF dimer + 2.25 mM unlabeled v107; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide90% H2O/10% D2O
41.0mM U-13C/15N labeled VEGF dimer + 2.25 mM unlabeled v107; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide100% D2O
50.6mM U-13C/15N labeled v107 + 0.45 mM unlabeled VEGF Dimer; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide, 15mg/ml pf1 phage90% H2O/10% D2O
61.0mM U-13C/15N labeled VEGF Dimer + 2.25 mM unlabeled v107; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide, 15mg/ml pf1 phage90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM sodium chloride, 20 sodium phosphate 7.0 1 atm308 K
250mM sodium chloride, 20 sodium phosphate 7.0 1 atm318 K
350mM sodium chloride, 20 sodium phosphate 7.0 1 atm298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker, Inc.collection
Felix98Accelys, Inc.processing
XEASY1.3.13Bartels, Xia, Billeter, Guntert, Wuthrichdata analysis
CNX2000.1Accelys, Inc.structure solution
CNX2000.1Accelys, Inc.refinement
RefinementMethod: Torsion angle dynamics simulated annealing / Software ordinal: 1
Details: The structures are based on 3940 NOE-derived distance restraints, 176 distance restraints from hydrogen bonds, 476 dihedral angle restraints, 146 residual dipolar coupling restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 120 / Conformers submitted total number: 24

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