7KPA: Asymmetric hTNF-alpha

asymmetric hTNF-alpha. Determined by X-ray diffraction at 2.3 Å resolution. Released 13 Jan 2021.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,275
Mol. weight: 52.93 kDa
Ligands: D84
Released: 13 Jan 2021

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

Secondary structure: helices and β-sheets

7KPA contains 6 α-helices and 37 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: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
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	113-119	7	1
β-strand	122-126	5	1
β-strand	131-136	6	2
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	76-83	8	4
β-strand	90-98	9	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: 3 helices, 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
α-helix	50	1
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
α-helix	147-149	3
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

>7KPA_1 Tumor necrosis factor (chains A, B, C)
SVRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIY
SQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIY
LGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL

Ligands and cofactors

ID	Name	Formula	Copies
D84	5-(1-{[2-(difluoromethoxy)phenyl]methyl}-2-{[3-(2-oxopyrrolidin-1-yl)phenoxy]me…	C31 H26 F2 N4 O4	1

Primary citation

A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF. Lightwood, D.J., Munro, R.J., Porter, J. et al. Nat Commun (2021) 12:583-583. DOI 10.1038/s41467-020-20825-6 · 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

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