Macromolecule Content

Total Structure Weight: 81.53 kDa
Atom Count: 4940
Residue Count: 673
Unique protein chains: 2

7KP8

asymmetric mTNF-alpha hTNFR1 complex

DOI: 10.2210/pdb7KP8/pdb

Classification: CYTOKINE
Organism(s): Mus musculus, Homo sapiens
Expression System: Escherichia coli, unidentified baculovirus
Mutation(s): Yes

Deposited: 2020-11-10 Released: 2021-01-13
Deposition Author(s): Arakaki, T.L., Fox III, D., Edwards, T.E., Foley, A., Ceska, T.

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
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor	A, B, C	147	Mus musculus	Mutation(s): 0 Gene Names: Tnf, Tnfa, Tnfsf2
Find proteins for P06804 (Mus musculus) Explore P06804 Go to UniProtKB: P06804
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 1A	E, F	142	Homo sapiens	Mutation(s): 2 Gene Names: TNFRSF1A, TNFAR, TNFR1
Find proteins for P19438 (Homo sapiens) Explore P19438 Go to UniProtKB: P19438
NIH Common Fund Data Resources
PHAROS P19438 GTEx ENSG00000067182
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A7G Query on A7G Download Ideal Coordinates CCD File SDF format, chain F [C] MOL2 format, chain F [C]	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 = 133.577	α = 90
b = 133.577	β = 90
c = 141.445	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
REFMAC	refinement
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2020-11-10
Released Date: 2021-01-13

Deposition Author(s):

Revision History

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

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.