6A3W Immune System date Jun 17, 2018
title Complex Structure Of 4-1bb And Utomilumab
authors Y.Li, S.Tan, C.Zhang, Y.Chai, J.Qi, P.Tien, S.Gao, G.F.Gao
compound source
Molecule: Utomilumab Vh
Chain: A, D, G, J
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Utomilumab Vl
Chain: B, E, H, K
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Tumor Necrosis Factor Receptor Superfamily Member
Chain: C, F, I, L
Synonym: 4-1bb Ligand Receptor,Cdw137,T-Cell Antigen 4-1bb Cell Antigen Ila;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfrsf9, Cd137, Ila
Expression_system: Baculovirus Transfer Vector Pfastbac1
Expression_system_taxid: 136645
symmetry Space Group: P 1 21 1
R_factor 0.185 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.727 184.604 90.205 90.00 104.04 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, C, I, L


Primary referenceLimited Cross-Linking of 4-1BB by 4-1BB Ligand and the Agonist Monoclonal Antibody Utomilumab., Li Y, Tan S, Zhang C, Chai Y, He M, Zhang CW, Wang Q, Tong Z, Liu K, Lei Y, Liu WJ, Liu Y, Tian Z, Cao X, Yan J, Qi J, Tien P, Gao S, Gao GF, Cell Rep. 2018 Oct 23;25(4):909-920.e4. doi: 10.1016/j.celrep.2018.09.073. PMID:30355497
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (445 Kb) [Save to disk]
  • Biological Unit Coordinates (6a3w.pdb1.gz) 118 Kb
  • Biological Unit Coordinates (6a3w.pdb2.gz) 105 Kb
  • Biological Unit Coordinates (6a3w.pdb3.gz) 116 Kb
  • Biological Unit Coordinates (6a3w.pdb4.gz) 113 Kb
  • LPC: Ligand-Protein Contacts for 6A3W
  • CSU: Contacts of Structural Units for 6A3W
  • Structure Factors (2921 Kb)
  • Retrieve 6A3W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6A3W from S2C, [Save to disk]
  • View 6A3W 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 6A3W
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6a3w from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6a3w_J] [6a3w_B] [6a3w_L] [6a3w_G] [6a3w_E] [6a3w_K] [6a3w_F] [6a3w_D] [6a3w_H] [6a3w_I] [6a3w_A] [6a3w_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6A3W
  • Community annotation for 6A3W at PDBWiki (http://pdbwiki.org)

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