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The crystal structure of zebrafish tumor necrosis factor alpha

Analyse The crystal structure of zebrafish tumor necrosis factor alpha in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DOV
Type: protein
Length: 444 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.59
Source: Danio rerio
Molecule: Lymphotoxin-alpha
UniProt: Q6T9C7
Pockets: 7 · best druggability 0.70

Structure

x-ray diffraction · resolution 2.59 · 1 distinct chain · 5% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Lymphotoxin-alpha	protein	148	5% helix, 52% strand	Q6T9C7

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.70	0.98	17	empty
2	151	0.54	0.81	25	empty
3	124	0.48	0.80	22	empty
4	94	0.48	0.81	18	empty
5	74	0.36	0.77	16	empty

Interfaces

3 interfaces between chains.

A–C · 1049 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1036 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1011 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7DOV · The crystal structure of zebrafish tumor necrosis factor alpha · 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 Q6T9C7
Elsewhere: RCSB PDB 7DOV · PDBe 7DOV · UniProt Q6T9C7

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