3KQ4 Transport Protein date Nov 17, 2009
title Structure Of Intrinsic Factor-Cobalamin Bound To Its Recepto
authors C.B.F.Andersen, M.Madsen, S.K.Moestrup, G.R.Andersen
compound source
Molecule: Gastric Intrinsic Factor
Chain: A, C, E
Fragment: Unp Residues 25-417
Synonym: Intrinsic Factor, Inf, If
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gif, Ifmh
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922

Molecule: Cubilin
Chain: B, D, F
Fragment: Unp Residues 932-1388
Synonym: Intrinsic Factor-Cobalamin Receptor, Intrinsic Fac Vitamin B12 Receptor, 460 Kda Receptor, Intestinal Intrinsi Receptor;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cubn, Ifcr
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
symmetry Space Group: C 2 2 21
R_factor 0.211 R_Free 0.243
length a length b length c angle alpha angle beta angle gamma
117.684 204.179 410.023 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.30 Å
ligand B12, BMA, CA, MAN, NAG enzyme
A, C, E

Primary referenceStructural basis for receptor recognition of vitamin-B(12)-intrinsic factor complexes., Andersen CB, Madsen M, Storm T, Moestrup SK, Andersen GR, Nature. 2010 Mar 18;464(7287):445-8. PMID:20237569
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (899 Kb) [Save to disk]
  • Biological Unit Coordinates (3kq4.pdb1.gz) 299 Kb
  • Biological Unit Coordinates (3kq4.pdb2.gz) 300 Kb
  • Biological Unit Coordinates (3kq4.pdb3.gz) 301 Kb
  • LPC: Ligand-Protein Contacts for 3KQ4
  • CSU: Contacts of Structural Units for 3KQ4
  • Structure Factors (605 Kb)
  • Retrieve 3KQ4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KQ4 from S2C, [Save to disk]
  • Re-refined 3kq4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KQ4 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 3KQ4
  • 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 3KQ4, from MSDmotif at EBI
  • Fold representative 3kq4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kq4] [3kq4_E] [3kq4_D] [3kq4_B] [3kq4_A] [3kq4_C] [3kq4_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3KQ4: [CUB ] by SMART
  • Other resources with information on 3KQ4
  • Community annotation for 3KQ4 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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