4KV5 Immune System date May 22, 2013
title Scfv Gc1009 In Complex With Tgf-Beta1.
authors R.Wei, A.G.Moulin, M.Mathieu
compound source
Molecule: Transforming Growth Factor Beta-1 Proprotein
Chain: C, D, A, B
Fragment: Unp Residues 279-390
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tgfb1, Tgfb
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Single-Chain Variable Fragment Gc1009
Chain: J, H, E, G
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Origami2 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet25b
symmetry Space Group: C 1 2 1
R_factor 0.229 R_Free 0.300
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.188 171.769 109.876 90.00 111.30 90.00
method X-Ray Diffractionresolution 3.00 Å
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructures of a pan-specific antagonist antibody complexed to different isoforms of TGFbeta reveal structural plasticity of antibody-antigen interactions., Moulin A, Mathieu M, Lawrence C, Bigelow R, Levine M, Hamel C, Marquette JP, Le Parc J, Loux C, Ferrari P, Capdevila C, Dumas J, Dumas B, Rak A, Bird J, Qiu H, Pan CQ, Edmunds T, Wei RR, Protein Sci. 2014 Sep 10. doi: 10.1002/pro.2548. PMID:25209176
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (221 Kb) [Save to disk]
  • Biological Unit Coordinates (4kv5.pdb1.gz) 41 Kb
  • Biological Unit Coordinates (4kv5.pdb2.gz) 40 Kb
  • Biological Unit Coordinates (4kv5.pdb3.gz) 39 Kb
  • Biological Unit Coordinates (4kv5.pdb4.gz) 39 Kb
  • Biological Unit Coordinates (4kv5.pdb5.gz) 39 Kb
  • Biological Unit Coordinates (4kv5.pdb6.gz) 39 Kb
  • CSU: Contacts of Structural Units for 4KV5
  • Structure Factors (265 Kb)
  • Retrieve 4KV5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KV5 from S2C, [Save to disk]
  • Re-refined 4kv5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KV5 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 4KV5
  • 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 4KV5, from MSDmotif at EBI
  • Fold representative 4kv5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kv5_F] [4kv5_B] [4kv5] [4kv5_G] [4kv5_A] [4kv5_E] [4kv5_H] [4kv5_K] [4kv5_D] [4kv5_C] [4kv5_L] [4kv5_J] [4kv5_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4KV5: [IGv] [TGFB ] by SMART
  • Other resources with information on 4KV5
  • Community annotation for 4KV5 at PDBWiki (http://pdbwiki.org)

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