6MGP

Structure of human 4-1BB / 4-1BBL complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.217 

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

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

(2018) Nat Commun 9: 4679-4691


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor ligand superfamily member 9
A, B, C
207Homo sapiensMutation(s): 0 
Gene Names: TNFSF9
Find proteins for P41273 (Homo sapiens)
Go to Gene View: TNFSF9
Go to UniProtKB:  P41273
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor receptor superfamily member 9
X, Y, Z
144Homo 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
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, C, X, Y
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, C, Z
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 
X, Y, Z
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.217 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 102.013α = 90.00
b = 229.378β = 90.00
c = 114.900γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release