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Structure of zebrafish TRAF6 in complex with sting ctt

Analyse Structure of zebrafish TRAF6 in complex with sting ctt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MYD
Type: protein
Length: 322 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TNF receptor-associated factor 6; Sting ctt, transmembrane protein 173
EC: 2.3.2.27
UniProt: Q6IWL4, E7F4N7
Ligands: SO4
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TNF receptor-associated factor 6 (EC 2.3.2.27)	protein	155	17% helix, 40% strand	Q6IWL4
B, D	Sting ctt, transmembrane protein 173	protein	8	0% helix, 50% strand	E7F4N7
C	TNF receptor-associated factor 6 (EC 2.3.2.27)	protein	151	15% helix, 41% strand	Q6IWL4

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, C

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

Pockets

5 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	237	0.69	0.85	31	empty
2	267	0.64	0.81	35	empty
3	298	0.61	0.79	33	empty
4	55	0.29	0.75	16	empty
5	51	0.27	0.74	15	empty

Interfaces

5 interfaces between chains.

C–D · 572 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 565 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 549 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 131 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 22 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6MYD · Structure of zebrafish TRAF6 in complex with STING CTT · the same entry in another collection · chain A against A, TM-score 1.00
Q6IWL4 · AlphaFold monomer V2.0 prediction for TNF receptor-associated factor 6 (Q6IWL4) · a predicted model of the same protein · chain C against A, TM-score 0.96
E7F4N7 · AlphaFold monomer V2.0 prediction for stimulator of interferon genes protein (E7F4N7) · a predicted model of the same protein · chain B against A, TM-score 0.48

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 Q6IWL4
Every structure of UniProt E7F4N7
Elsewhere: RCSB PDB 6MYD · PDBe 6MYD · UniProt Q6IWL4 · UniProt E7F4N7

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