5M2J: Complex between human TNF alpha and Llama VHH2

Complex between human TNF alpha and Llama VHH2. Determined by X-ray diffraction at 1.9 Å resolution. Released 30 Aug 2017.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,315
Mol. weight: 29.99 kDa
Released: 30 Aug 2017

Explore 5M2J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M2J contains 3 α-helices and 24 β-strands across 2 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: 1 helix, 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
β-strand	54-66	13	1
β-strand	76-83	8	2
β-strand	90-98	9	2
β-strand	114-126	13	1
β-strand	131-136	6	2
α-helix	139-141	3
β-strand	142	1	1
β-strand	151-156	6	1

Chain D: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	3
β-strand	11-12	2	4
β-strand	18-25	8	3
α-helix	29-31	3
β-strand	32	1	2
β-strand	34-39	6	5
β-strand	46-51	6	5
β-strand	58-59	2	5
β-strand	68-73	6	3
β-strand	78-83	6	3
α-helix	88-90	3
β-strand	92-97	6	5
β-strand	109-111	3	5
β-strand	112-113	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor	A	protein	157	Homo sapiens	P01375 (AlphaFold model)
Anti-(ED-B) scFV	D	protein	115	Homo sapiens

Sequence of entity 1 (A), FASTA

>5M2J_1 Tumor necrosis factor (chains A)
VRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYS
QVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYL
GGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL

Sequence of entity 2 (D), FASTA

>5M2J_2 Anti-(ED-B) scFV (chains D)
QVQLVESGGGLVQPGGSLRLSCAASGFTFSNYWMYWVRQAPGKGLEWVSEINTNGLITKY
PDSVKGRFTISRDNAKNTLYLQMNSLKPEDTALYYCARSPSGFNRGQGTQVTVSS

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
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
7KP9 2.15 Å, asymmetric hTNF-alpha

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