2QQM 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-1
Chain: A
Fragment: Cub 2, F58 Type C 1, And F58 Type C 2 Domains
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: 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 0.183 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.177 68.178 66.613 90.00 102.10 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand CA, EDO, FUC, 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] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (2qqm.pdb1.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 2QQM
  • CSU: Contacts of Structural Units for 2QQM
  • Likely Quarternary Molecular Structure file(s) for 2QQM
  • Structure Factors (225 Kb)
  • Retrieve 2QQM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2QQM from S2C, [Save to disk]
  • Re-refined 2qqm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2QQM 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 2QQM
  • 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 2QQM, from MSDmotif at EBI
  • Fold representative 2qqm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2qqm_A] [2qqm]
  • SWISS-PROT database: [O14786]
  • Domain organization of [NRP1_HUMAN] by SWISSPFAM
  • Domains found in 2QQM: [CUB] [FA58C ] by SMART
  • Other resources with information on 2QQM
  • Community annotation for 2QQM 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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