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Cryoem structure of HRD3/YOS9 complex

Analyse Cryoem structure of HRD3/YOS9 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VK3
Type: protein
Length: 961 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HRD3; Protein os-9 homolog
UniProt: Q99220
Pockets: 18 · best druggability 0.71

Structure

electron microscopy · 2 distinct chains · 48% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HRD3	protein	611	65% helix, 1% strand	—
B	Protein os-9 homolog	protein	350	19% helix, 32% strand	Q99220

Pockets

18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	569	0.71	0.80	55	empty
2	719	0.69	0.77	52	empty
3	265	0.66	0.82	41	empty
4	201	0.63	0.83	23	empty
5	236	0.58	0.79	29	empty

Interfaces

1 interface between chains.

A–B · 2664 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6VK3 · CryoEM structure of Hrd3/Yos9 complex · the same entry in another collection · chain A against A, TM-score 1.00
Q99220 · AlphaFold monomer V2.0 prediction for protein os-9 homolog (Q99220) · a predicted model of the same protein · chain B against A, TM-score 0.59

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 Q99220
Elsewhere: RCSB PDB 6VK3 · PDBe 6VK3 · UniProt Q99220

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