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Crystal structure of TRAF4 traf domain

Analyse Crystal structure of TRAF4 traf domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4K8U
Type: protein
Length: 530 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TNF receptor-associated factor 4
UniProt: Q9BUZ4
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 13% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TNF receptor-associated factor 4	protein	178	16% helix, 31% strand	Q9BUZ4
B	TNF receptor-associated factor 4	protein	176	13% helix, 31% strand	Q9BUZ4
C	TNF receptor-associated factor 4	protein	176	10% helix, 31% strand	Q9BUZ4

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	987	0.78	0.79	78	empty
2	246	0.56	0.77	27	empty
3	222	0.55	0.77	24	empty
4	215	0.47	0.74	22	empty
5	149	0.46	0.77	23	empty

Interfaces

3 interfaces between chains.

A–B · 763 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 711 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 637 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4K8U · Crystal structure of TRAF4 TRAF domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9BUZ4 · AlphaFold monomer V2.0 prediction for TNF receptor-associated factor 4 (Q9BUZ4) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q9BUZ4
Elsewhere: RCSB PDB 4K8U · PDBe 4K8U · UniProt Q9BUZ4

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