2QQK 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: C 1 2 1
R_factor 0.186 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
148.277 105.873 92.400 90.00 98.83 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand NAG enzyme
Primary referenceStructural 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] (159 Kb) [Save to disk]
  • Biological Unit Coordinates (2qqk.pdb1.gz) 301 Kb
  • Biological Unit Coordinates (2qqk.pdb2.gz) 152 Kb
  • LPC: Ligand-Protein Contacts for 2QQK
  • CSU: Contacts of Structural Units for 2QQK
  • Likely Quarternary Molecular Structure file(s) for 2QQK
  • Structure Factors (276 Kb)
  • Retrieve 2QQK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2QQK from S2C, [Save to disk]
  • Re-refined 2qqk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2QQK 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 2QQK
  • 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 2QQK, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2qqk] [2qqk_H] [2qqk_L] [2qqk_A]
  • SWISS-PROT database: [P01857] [P01834] [O60462]
  • Domain organization of [IGHG1_HUMAN] [IGKC_HUMAN] [NRP2_HUMAN] by SWISSPFAM
  • Domains found in 2QQK: [CUB] [FA58C] [IG_like] [IGv ] by SMART
  • Other resources with information on 2QQK
  • Community annotation for 2QQK at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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