5DN2	Signaling Protein	date	Sep 09, 2015
title	Human Nrp2 B1 Domain In Complex With The Peptide Correspondi C-Terminus Of Vegf-A
authors	Y.C.I.Tsai, P.Frankel, C.Fotinou, R.Rana, I.Zachary, S.Djordjevic
compound		source
Molecule: Neuropilin-2 Chain: A, B, C, D Fragment: Neuropilin-2 Domain B1 F58 Type C 1, Unp Residue Synonym: Vascular Endothelial Cell Growth Factor 165 Recept Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Nrp2, Vegf165r2 Expression_system: Escherichia Coli Expression_system_taxid: 83333 Expression_system_strain: K-12 Expression_system_variant: Rosetta-Gami 2(De3)Plyss Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet15b-Tev
Molecule: Vascular Endothelial Growth Factor A Chain: F, G, E Fragment: Vegf-A165-Hbd, Unp Residues 205-232 Synonym: Vegf-A,Vascular Permeability Factor,Vpf Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Vegfa, Vegf Expression_system: Escherichia Coli Expression_system_taxid: 83333 Expression_system_strain: K-12 Expression_system_variant: Shuffle Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet14b
symmetry	Space Group: C 2 2 21	R_factor 0.204 R_Free 0.234
crystal cell	length a length b length c angle alpha angle beta angle gamma 110.250 139.520 106.040 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.95 Å
ligand	DIO, GOL	enzyme
Gene Ontology	Chain Function Process Component A, D, C, B F, G, E
Primary reference	Structural studies of neuropilin-2 reveal a zinc ion binding site remote from the vascular endothelial growth factor binding pocket., Tsai YC, Fotinou C, Rana R, Yelland T, Frankel P, Zachary I, Djordjevic S, FEBS J. 2016 May;283(10):1921-34. doi: 10.1111/febs.13711. Epub 2016 Apr 1. PMID:26991001

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (215 Kb) [Save to disk] Biological Unit Coordinates (5dn2.pdb1.gz) 54 Kb Biological Unit Coordinates (5dn2.pdb2.gz) 53 Kb Biological Unit Coordinates (5dn2.pdb3.gz) 54 Kb Biological Unit Coordinates (5dn2.pdb4.gz) 54 Kb LPC: Ligand-Protein Contacts for 5DN2 CSU: Contacts of Structural Units for 5DN2 Structure Factors (3134 Kb) Retrieve 5DN2 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5DN2 from S2C, [Save to disk] Re-refined 5dn2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5DN2 in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 5DN2

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5dn2_A] [5dn2_E] [5dn2_B] [5dn2] [5dn2_G] [5dn2_F] [5dn2_D] [5dn2_C] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 5DN2: [FA58C ] by SMART

Other resources with information on 5DN2

Community annotation for 5DN2 at PDBWiki (http://pdbwiki.org)

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