Research workbench

Structure of the A20 ovarian tumour (otu) domain

Analyse Structure of the A20 ovarian tumour (otu) domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VFJ
Type: protein
Length: 1,303 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor
EC: 3.4.19.12
UniProt: P21580
Ligands: MG, SO4
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tumor necrosis factor (EC 3.4.19.12)	protein	330	39% helix, 18% strand	P21580
B	Tumor necrosis factor (EC 3.4.19.12)	protein	317	41% helix, 16% strand	P21580
C	Tumor necrosis factor (EC 3.4.19.12)	protein	327	39% helix, 16% strand	P21580
D	Tumor necrosis factor (EC 3.4.19.12)	protein	329	39% helix, 16% strand	P21580

Ligands and binding sites

MG · Magnesium ion · metal · chains C, D
SO4 · Sulfate ion · ion · 4 copies · chains C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	946	0.76	0.79	79	SO4
2	247	0.63	0.81	43	empty
3	65	0.54	0.87	23	empty
4	306	0.53	0.75	41	SO4
5	66	0.51	0.86	24	empty

Interfaces

4 interfaces between chains.

A–D · 579 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 577 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 415 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 341 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2VFJ · Structure of the A20 Ovarian Tumour (OTU) domain · the same entry in another collection · chain D against D, TM-score 1.00
P21580 · AlphaFold monomer V2.0 prediction for tumor necrosis factor alpha- induced protein 3… · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P21580
Elsewhere: RCSB PDB 2VFJ · PDBe 2VFJ · UniProt P21580

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.