2QQL	Signaling Protein	date	Jul 26, 2007
title	Neuropilin-2 A1a2b1b2 Domains In Complex With A Semaphorin-B Fab
authors	B.A.Appleton, C.Wiesmann
compound		source
Molecule: Neuropilin-2 Chain: A Fragment: Cub 1, Cub2, F58 Type C 1, And C2 Domains 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: Trichoplusia Ni Expression_system_common: Cabbage Looper Expression_system_taxid: 7111 Expression_system_vector_type: Baculovirus
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: P 32 2 1	R_factor 0.188 R_Free 0.232
crystal cell	length a length b length c angle alpha angle beta angle gamma 121.406 121.406 202.717 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	3.10 Å
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] (161 Kb) [Save to disk] Biological Unit Coordinates (2qql.pdb1.gz) 304 Kb Biological Unit Coordinates (2qql.pdb2.gz) 154 Kb CSU: Contacts of Structural Units for 2QQL Likely Quarternary Molecular Structure file(s) for 2QQL Structure Factors (238 Kb) Retrieve 2QQL in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2QQL from S2C, [Save to disk] Re-refined 2qql structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2QQL 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 2QQL

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 2QQL, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2qql] [2qql_A] [2qql_H] [2qql_L] SWISS-PROT database: [P01857] [P01834] [O60462] Domain organization of [IGHG1_HUMAN] [IGKC_HUMAN] [NRP2_HUMAN] by SWISSPFAM Domains found in 2QQL: [CUB] [FA58C] [IG_like] [IGv ] by SMART

Other resources with information on 2QQL

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

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