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 0.242
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] (900 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
  • Alignments of the sequence of 3KQ4 with the sequences similar proteins can be viewed for 3KQ4's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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