6MI2

Structure of the human 4-1BB / Utomilumab Fab complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of the 4-1BB/4-1BBL complex and distinct binding and functional properties of utomilumab and urelumab.

Chin, S.M.Kimberlin, C.R.Roe-Zurz, Z.Zhang, P.Xu, A.Liao-Chan, S.Sen, D.Nager, A.R.Oakdale, N.S.Brown, C.Wang, F.Yang, Y.Lindquist, K.Yeung, Y.A.Salek-Ardakani, S.Chaparro-Riggers, J.

(2018) Nat Commun 9: 4679-4679


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Utomilumab Fab heavy chain
A, D
230N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Utomilumab Fab lambda chain
B, E
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor receptor superfamily member 9
F, C
145Homo sapiensMutation(s): 0 
Gene Names: TNFRSF9 (CD137, ILA)
Find proteins for Q07011 (Homo sapiens)
Go to Gene View: TNFRSF9
Go to UniProtKB:  Q07011
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
F
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
C, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.238 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 136.903α = 90.00
b = 73.338β = 98.99
c = 175.121γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release