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Crystal structure of the traf domain of TRAF2 in a complex with a peptide from the CD40 receptor

Analyse Crystal structure of the traf domain of TRAF2 in a complex with a peptide from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QSC
Type: protein
Length: 555 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TNF receptor associated factor 2; CD40 receptor
UniProt: Q12933
Ligands: ACE
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	TNF receptor associated factor 2	protein	179	22% helix, 31% strand	Q12933
D, E, F	CD40 receptor	protein	6	0% helix, 33% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 3 copies · chains A, D, B, E, C, F

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

Pockets

5 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	953	0.75	0.78	85	empty
2	219	0.54	0.77	24	empty
3	103	0.39	0.76	23	empty
4	109	0.37	0.74	24	empty
5	100	0.36	0.74	24	empty

Interfaces

6 interfaces between chains.

B–C · 856 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 816 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 765 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 498 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 489 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 modified, 3 covalent (engineered, covalent ligand).

Compared structures

1QSC · Crystal structure of the traf domain of TRAF2 in a complex with a peptide from the CD40… · the same entry in another collection · chain C against C, TM-score 1.00
Q12933 · AlphaFold monomer V2.0 prediction for TNF receptor-associated factor 2 (Q12933) · 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 Q12933
Elsewhere: RCSB PDB 1QSC · PDBe 1QSC · UniProt Q12933

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