3KR3 Immune System date Nov 17, 2009
title Crystal Structure Of Igf-II Antibody Complex
authors T.S.Peat, J.Newman, T.E.Adams
compound source
Molecule: Insulin-Like Growth Factor II
Chain: D
Synonym: Igf-II, Somatomedin-A
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Igf-II, Igf2, Pp1446
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector: Novozyme Proprietary

Molecule: Antibody-Fab (Heavy Chain)
Chain: H
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector: Phagemid Vector Pmid21

Molecule: Antibody-Fab (Light Chain)
Chain: L
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector: Phagemid Vector Pmid21
symmetry Space Group: P 21 21 21
R_factor 0.199 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.667 106.921 110.657 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand EDO enzyme
Primary referenceA human monoclonal antibody against insulin-like growth factor-II blocks the growth of human hepatocellular carcinoma cell lines in vitro and in vivo., Dransfield DT, Cohen EH, Chang Q, Sparrow LG, Bentley JD, Dolezal O, Xiao X, Peat TS, Newman J, Pilling PA, Phan T, Priebe I, Brierley GV, Kastrapeli N, Kopacz K, Martik D, Wassaf D, Rank D, Conley G, Huang Y, Adams TE, Cosgrove L, Mol Cancer Ther. 2010 Jun;9(6):1809-19. Epub 2010 Jun 1. PMID:20515953
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (87 Kb) [Save to disk]
  • Biological Unit Coordinates (3kr3.pdb1.gz) 82 Kb
  • LPC: Ligand-Protein Contacts for 3KR3
  • CSU: Contacts of Structural Units for 3KR3
  • Structure Factors (1407 Kb)
  • Retrieve 3KR3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KR3 from S2C, [Save to disk]
  • Re-refined 3kr3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KR3 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 3KR3
  • 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 3KR3, from MSDmotif at EBI
  • Fold representative 3kr3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kr3_L] [3kr3_H] [3kr3] [3kr3_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3KR3: [IGc1] [IGv] [IlGF ] by SMART
  • Alignments of the sequence of 3KR3 with the sequences similar proteins can be viewed for 3KR3'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 3KR3
  • Community annotation for 3KR3 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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