7KP8

asymmetric mTNF-alpha hTNFR1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report



Literature

Structural insights into disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF

McMillan, D.Martinez-Fleites, C.Porter, J.Fox III, D.Davis, R.Mori, P.Ceska, T.Carrington, B.Lawson, A.Bourne, T.O'Connell, J.

(2020) Nat Commun 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor necrosis factorABC147Mus musculusMutation(s): 0 
Gene Names: TnfTnfaTnfsf2
Find proteins for P06804 (Mus musculus)
Explore P06804 
Go to UniProtKB:  P06804
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 1AEF142Homo sapiensMutation(s): 2 
Gene Names: TNFRSF1ATNFARTNFR1
Find proteins for P19438 (Homo sapiens)
Explore P19438 
Go to UniProtKB:  P19438
NIH Common Fund Data Resources
PHAROS  P19438
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A7G
Query on A7G

Download Ideal Coordinates CCD File 
C
1-{[2-(difluoromethoxy)phenyl]methyl}-2-methyl-6-[6-(piperazin-1-yl)pyridin-3-yl]-1H-benzimidazole
C25 H25 F2 N5 O
LRHACCJNWLLTDS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.577α = 90
b = 133.577β = 90
c = 141.445γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2021-01-13
    Type: Initial release