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Structure of TNF receptor associated factor 2 (TRAF2) in complex with a human OX40 peptide

Analyse Structure of TNF receptor associated factor 2 (TRAF2) in complex with a human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1D0A
Type: protein
Length: 1,038 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor receptor associated protein 2; OX40L receptor peptide
UniProt: Q12933, P43489
Ligands: ACE
Pockets: 8 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Tumor necrosis factor receptor associated protein 2	protein	168	21% helix, 33% strand	Q12933
G, H, I, J, K, L	OX40L receptor peptide	protein	5	0% helix, 40% strand	P43489

Ligands and binding sites

ACE · Acetyl group · ligand · 6 copies · chains A, G, B, H, I, D, J, E, K, F, L

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

Pockets

8 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	1077	0.74	0.77	81	empty
2	1040	0.74	0.77	84	empty
3	123	0.40	0.74	24	empty
4	113	0.37	0.74	19	empty
5	108	0.37	0.74	21	empty

Interfaces

12 interfaces between chains.

A–C · 579 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 577 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 576 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 575 Å² buried · 4 hydrogen bonds · protein-protein
D–F · 565 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent (covalent ligand).

Compared structures

1D0A · Structure of TNF receptor associated factor 2 (TRAF2) in complex with a human OX40 peptide · the same entry in another collection · chain L against L, 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 Q12933
Every structure of UniProt P43489
Elsewhere: RCSB PDB 1D0A · PDBe 1D0A · UniProt Q12933 · UniProt P43489

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