MolNFT v1 · #126421 · protein

Complex between human TNF alpha and llama VHH2

5M2J · Tumor necrosis factor: “Complex between human TNF alpha and llama VHH2”. X-ray diffraction, 2 pockets (best druggability 0.48). MolNFT v1 #126421 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5M2J
Type: protein
Length: 254 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor; Anti-(ed-B) scfv
UniProt: P01375
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tumor necrosis factor	protein	139	2% helix, 53% strand	P01375
D	Anti-(ed-B) scfv	protein	115	5% helix, 46% strand	—

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	217	0.48	0.74	29	empty
2	56	0.34	0.78	15	empty

Interfaces

1 interface between chains.

A–D · 604 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5M2J · Complex between human TNF alpha and Llama VHH2 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P01375
Elsewhere: RCSB PDB 5M2J · PDBe 5M2J · UniProt P01375

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