2QQO Signaling Protein date Jul 26, 2007
title Crystal Structure Of The A2b1b2 Domains From Human Neuropili
authors B.A.Appleton, C.Wiesmann
compound source
Molecule: Neuropilin-2
Chain: A, B
Fragment: Cub 2, F58 Type C 1, And F58 Type C 2 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
symmetry Space Group: P 1 21 1
R_factor 0.185 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.093 192.909 66.169 90.00 90.08 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand CA, EDO, TRS enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


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] (154 Kb) [Save to disk]
  • Biological Unit Coordinates (2qqo.pdb1.gz) 76 Kb
  • Biological Unit Coordinates (2qqo.pdb2.gz) 75 Kb
  • Biological Unit Coordinates (2qqo.pdb3.gz) 147 Kb
  • LPC: Ligand-Protein Contacts for 2QQO
  • CSU: Contacts of Structural Units for 2QQO
  • Likely Quarternary Molecular Structure file(s) for 2QQO
  • Structure Factors (399 Kb)
  • Retrieve 2QQO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2QQO from S2C, [Save to disk]
  • Re-refined 2qqo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2QQO 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 2QQO
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2QQO, from MSDmotif at EBI
  • Fold representative 2qqo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2qqo] [2qqo_B] [2qqo_A]
  • SWISS-PROT database: [O60462]
  • Domain organization of [NRP2_HUMAN] by SWISSPFAM
  • Domains found in 2QQO: [CUB] [FA58C ] by SMART
  • Other resources with information on 2QQO
  • Community annotation for 2QQO 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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