MolNFT v1 · #117226 · protein

Crystal structure of TRAF1 traf domain

5E1T · TNF receptor-associated factor 1: “Crystal structure of TRAF1 traf domain”. X-ray diffraction, 5 pockets (best druggability 0.75). MolNFT v1 #117226 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5E1T
Type: protein
Length: 569 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TNF receptor-associated factor 1
UniProt: Q13077
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TNF receptor-associated factor 1	protein	192	29% helix, 30% strand	Q13077
B	TNF receptor-associated factor 1	protein	191	32% helix, 29% strand	Q13077
C	TNF receptor-associated factor 1	protein	186	30% helix, 30% strand	Q13077

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1106	0.75	0.78	100	empty
2	65	0.30	0.74	15	empty
3	52	0.30	0.76	17	empty
4	50	0.26	0.74	16	empty
5	51	0.25	0.73	14	empty

Interfaces

3 interfaces between chains.

B–C · 1320 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1217 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 1115 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5E1T · Crystal structure of TRAF1 TRAF domain · the same entry in another collection · chain A against A, TM-score 1.00
Q13077 · AlphaFold monomer V2.0 prediction for TNF receptor-associated factor 1 (Q13077) · a predicted model of the same protein · chain C 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 Q13077
Elsewhere: RCSB PDB 5E1T · PDBe 5E1T · UniProt Q13077

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