2V5P Receptor Glycoprotein date Jul 06, 2007
title Complex Structure Of Human Igf2r Domains 11-13 Bound To Igf-II
authors J.Brown, C.Delaine, O.J.Zaccheo, C.Siebold, R.J.Gilbert, G.Van Boxel, A.Denley, J.C.Wallace, A.B.Hassan, B.E.Forbes, E.Y.Jones
compound source
Molecule: Cation-Independent Mannose-6-Phosphate Receptor
Chain: A, B
Fragment: Domains 11-13, Residues 1508-1992
Synonym: Insulin-Like Growth Factor II Receptor, Ci Man-6-P Receptor, Ci-Mpr, M6pr, Insulin-Like Growth Factor 2 Receptor, Igf-II Receptor, M6pigf2 Receptor, M6pigf2r, 300 Kda Mannose 6-Phosphate Receptor, Mpr 300, Mpr300, Cd222 Antigen;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Atcc: 95661
Organ: Placenta
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
Expression_system_strain: Lecr
Expression_system_variant: 3.2.8.1
Expression_system_plasmid: Pee14

Molecule: Insulin-Like Growth Factor II
Chain: C, D
Synonym: Igf-II, Somatomedin A
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm101
Expression_system_plasmid: Pgem-Teasy
symmetry Space Group: C 1 2 1
R_factor 0.291 R_Free 0.327
crystal
cell
length a length b length c angle alpha angle beta angle gamma
165.979 117.312 116.668 90.00 123.41 90.00
method X-Ray Diffractionresolution 4.10 Å
ligand BMA, NAG enzyme
Primary referenceStructure and functional analysis of the IGF-II/IGF2R interaction., Brown J, Delaine C, Zaccheo OJ, Siebold C, Gilbert RJ, van Boxel G, Denley A, Wallace JC, Hassan AB, Forbes BE, Jones EY, EMBO J. 2007 Nov 29;. PMID:18046459
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (337 Kb) [Save to disk]
  • Biological Unit Coordinates (2v5p.pdb1.gz) 167 Kb
  • Biological Unit Coordinates (2v5p.pdb2.gz) 167 Kb
  • LPC: Ligand-Protein Contacts for 2V5P
  • CSU: Contacts of Structural Units for 2V5P
  • Likely Quarternary Molecular Structure file(s) for 2V5P
  • Structure Factors (125 Kb)
  • Retrieve 2V5P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2V5P from S2C, [Save to disk]
  • Re-refined 2v5p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2V5P 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 2V5P
  • 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 2V5P, from MSDmotif at EBI
  • Fold representative 2v5p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2v5p_B] [2v5p_D] [2v5p] [2v5p_C] [2v5p_A]
  • SWISS-PROT database: [P01344] [P11717]
  • Domain organization of [IGF2_HUMAN] [MPRI_HUMAN] by SWISSPFAM
  • Domains found in 2V5P: [FN2] [IlGF ] by SMART
  • Other resources with information on 2V5P
  • Community annotation for 2V5P 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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