5M2I: Human Tumor Necrosis Factor

Structure of human Tumor Necrosis Factor (TNF) in complex with the Llama VHH1. Determined by X-ray diffraction at 2.15 Å resolution. Released 30 Aug 2017.

Method: X-ray diffraction
Resolution: 2.15 Å
Organisms: Homo sapiens, Lama glama
Chains: 12
Atoms: 13,256
Mol. weight: 184.72 kDa
Released: 30 Aug 2017

Explore 5M2I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M2I contains 38 α-helices and 146 β-strands across 12 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.

Chains A and C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
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
α-helix	50	1
β-strand	54-67	14	1
β-strand	76-84	9	2
β-strand	89-98	10	2
α-helix	104-106	3
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

Chains D and E: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	7
β-strand	28-29	2	7
β-strand	36-38	3	7
β-strand	42-44	3	8
β-strand	47-49	3	8
α-helix	50	1
β-strand	54-67	14	7
β-strand	76-84	9	8
β-strand	89-98	10	8
β-strand	113-126	14	7
β-strand	131-136	6	8
α-helix	139-141	3
β-strand	142	1	7
β-strand	151-156	6	7

Chain F: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	11
β-strand	28-29	2	11
β-strand	36-38	3	11
β-strand	42-44	3	12
β-strand	47-49	3	12
α-helix	50	1
β-strand	54-67	14	11
β-strand	76-84	9	12
β-strand	89-98	10	12
α-helix	104-106	3
β-strand	107	1	13
β-strand	109	1	13
β-strand	113-126	14	11
β-strand	131-136	6	12
α-helix	139-141	3
β-strand	142	1	11
β-strand	151-156	6	11

Chains G, H, I, J, K and L: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	10-12	3	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	33-39	7	15
β-strand	46-51	6	15
α-helix	53-55	3
β-strand	58-60	3	15
α-helix	62-64	3
β-strand	65	1	14
β-strand	68-73	6	14
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	92-99	8	15
β-strand	111-113	3	15
β-strand	117-121	5	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor	A, B, C, D, E, F	protein	157	Homo sapiens	P01375 (AlphaFold model)
VHH1	G, H, I, J, K, L	protein	121	Lama glama

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>5M2I_1 Tumor necrosis factor (chains A, B, C, D, E, F)
VRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYS
QVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYL
GGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL

Sequence of entity 2 (G, H, I, J, K, L), FASTA

>5M2I_2 VHH1 (chains G, H, I, J, K, L)
VQLVESGGGLVQAGGSLSLSCSASGRSLSNYYMGWFRQAPGKERELLGNISWRGYNIYYK
DSVKGRFTISRDDAKNTIYLQMNRLKPEDTAVYYCAASILPLSDDPGWNTYWGQGTQVTV
S

Primary citation

Bivalent Llama Single-Domain Antibody Fragments against Tumor Necrosis Factor Have Picomolar Potencies due to Intramolecular Interactions. Beirnaert, E., Desmyter, A., Spinelli, S. et al. Front Immunol (2017) 8:867-867. DOI 10.3389/fimmu.2017.00867 · 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…
7KP9 2.15 Å, asymmetric hTNF-alpha

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