7KP9: Asymmetric hTNF-alpha

asymmetric hTNF-alpha. Determined by X-ray diffraction at 2.15 Å resolution. Released 13 Jan 2021.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,373
Mol. weight: 52.82 kDa
Ligands: A7G
Released: 13 Jan 2021

Explore 7KP9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KP9 contains 5 α-helices and 36 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
β-strand	13-18	6	1
β-strand	28-29	2	1
β-strand	36-38	3	1
β-strand	42-44	3	2
β-strand	47-49	3	2
β-strand	54-67	14	1
α-helix	73-74	2
β-strand	76-84	9	2
β-strand	87-98	12	2
β-strand	113-126	14	1
β-strand	131-136	6	2
α-helix	139-141	3
β-strand	142	1	1
β-strand	151-156	6	1

Chain B: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	3
β-strand	28-29	2	3
β-strand	36-38	3	3
β-strand	42-44	3	4
β-strand	47-49	3	4
β-strand	54-67	14	3
β-strand	76-84	9	4
β-strand	89-98	10	4
β-strand	113-126	14	3
β-strand	131-136	6	4
α-helix	139-141	3
β-strand	142	1	3
β-strand	151-156	6	3

Chain C: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	5
β-strand	28-29	2	5
β-strand	36-38	3	5
β-strand	42-44	3	6
β-strand	47-49	3	6
β-strand	54-67	14	5
β-strand	76-83	8	6
β-strand	90-98	9	6
β-strand	113-126	14	5
β-strand	131-136	6	6
α-helix	139-141	3
β-strand	142	1	5
β-strand	151-156	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor	A, B, C	protein	158	Homo sapiens	P01375 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>7KP9_1 Tumor necrosis factor (chains A, B, C)
SVRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIY
SQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIY
LGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL

Ligands and cofactors

ID	Name	Formula	Copies
A7G	1-{[2-(difluoromethoxy)phenyl]methyl}-2-methyl-6-[6-(piperazin-1-yl)pyridin-3-y…	C25 H25 F2 N5 O	1

Primary citation

Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF. McMillan, D., Martinez-Fleites, C., Porter, J. et al. Nat Commun (2021) 12:582-582. DOI 10.1038/s41467-020-20828-3 · PubMed

Other PDB entries of the same protein (UniProt P01375 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9OJO 1.36 Å, Crystal structure of TNF alpha in complex with compound 1
5UUI 1.4 Å, Crystal Structure of Spin-Labeled T77C TNFa
4Y6O 1.6 Å, Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr)
2E7A 1.8 Å, TNF Receptor Subtype One-selective TNF Mutant with Antagonistic Activity
4TSV 1.8 Å, High resolution crystal structure of a human tnf-alpha mutant
9OJS 1.85 Å, Crystal structure of TNF alpha in complex with compound 4
5M2J 1.9 Å, Complex between human TNF alpha and Llama VHH2
9BN7 1.92 Å, X-ray crystal structure of TNFa-VNAR C4 complex
2AZ5 2.1 Å, Crystal Structure of TNF-alpha with a small molecule inhibitor
3L9J 2.1 Å, Selection of a novel highly specific TNFalpha antagonist: Insight from the crystal…
7JRA 2.1 Å, HUMAN TNF-ALPHA IN COMPLEX WITH 2-[5-(3-chloro-4-{[(1R)-1-(2-fluorophenyl)ethyl]amino}qui…
5M2I 2.15 Å, Structure of human Tumor Necrosis Factor (TNF) in complex with the Llama VHH1

Browse structure collections

About this viewer

MolViewer shows 7KP9 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.