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TRAF4_GPIB complex

Analyse TRAF4_GPIB complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YC1
Type: protein
Length: 964 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TNF receptor-associated factor 4; Gpib peptide
UniProt: Q9BUZ4
Pockets: 11 · best druggability 0.69

Structure

x-ray diffraction · 7 distinct chains · 15% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TNF receptor-associated factor 4	protein	158	16% helix, 35% strand	Q9BUZ4
B	TNF receptor-associated factor 4	protein	149	15% helix, 37% strand	Q9BUZ4
C	TNF receptor-associated factor 4	protein	161	14% helix, 34% strand	Q9BUZ4
D	TNF receptor-associated factor 4	protein	161	16% helix, 34% strand	Q9BUZ4
E	TNF receptor-associated factor 4	protein	156	16% helix, 36% strand	Q9BUZ4
F	TNF receptor-associated factor 4	protein	164	13% helix, 34% strand	Q9BUZ4
G, I, K	Gpib peptide	protein	5	0% helix, 40% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	797	0.69	0.75	57	empty
2	667	0.68	0.76	54	empty
3	229	0.57	0.78	25	empty
4	211	0.53	0.77	25	empty
5	274	0.52	0.74	28	empty

Interfaces

10 interfaces between chains.

A–C · 651 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 635 Å² buried · 11 hydrogen bonds · protein-protein
D–F · 619 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 611 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 589 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5YC1 · TRAF4_GPIb complex · the same entry in another collection · chain K against K, 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 E against A, TM-score 0.98

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 5YC1 · PDBe 5YC1 · UniProt Q9BUZ4

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