2QQN	Signaling Protein	date	Jul 26, 2007
title	Neuropilin-1 B1 Domain In Complex With A Vegf-Blocking Fab
authors	B.A.Appleton, C.Wiesmann
compound		source
Molecule: Neuropilin-1 Chain: A Fragment: F58 Type C 1 Domain Synonym: Vascular Endothelial Cell Growth Factor 165 Recept Antigen; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Nrp1, Nrp, Vegf165r Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid
Molecule: Antibody Heavy Chain Chain: H Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid
Molecule: Antibody Light Chain Chain: L Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid
symmetry	Space Group: H 3	R_factor 0.159 R_Free 0.207
crystal cell	length a length b length c angle alpha angle beta angle gamma 214.115 214.115 45.465 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	EDO	enzyme
Primary reference	Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding., Appleton BA, Wu P, Maloney J, Yin J, Liang WC, Stawicki S, Mortara K, Bowman KK, Elliott JM, Desmarais W, Bazan JF, Bagri A, Tessier-Lavigne M, Koch AW, Wu Y, Watts RJ, Wiesmann C, EMBO J. 2007 Nov 8;. PMID:17989695

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (102 Kb) [Save to disk] Biological Unit Coordinates (2qqn.pdb1.gz) 96 Kb LPC: Ligand-Protein Contacts for 2QQN CSU: Contacts of Structural Units for 2QQN Likely Quarternary Molecular Structure file(s) for 2QQN Structure Factors (319 Kb) Retrieve 2QQN in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2QQN from S2C, [Save to disk] Re-refined 2qqn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2QQN 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 2QQN

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 3D motif for 2QQN, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2qqn_L] [2qqn_A] [2qqn] [2qqn_H] SWISS-PROT database: [P01857] [P01834] [O14786] Domain organization of [IGHG1_HUMAN] [IGKC_HUMAN] [NRP1_HUMAN] by SWISSPFAM Domains found in 2QQN: [FA58C] [IG_like] [IGv ] by SMART

Other resources with information on 2QQN

Community annotation for 2QQN at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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