Research workbench

S. cerevisiae HSP104:CASEIN complex, extended conformation

Analyse S. cerevisiae HSP104:CASEIN complex, extended conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VYA
Type: protein
Length: 3,502 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat shock protein 104; Alpha-S1-casein
UniProt: P31539
Ligands: AGS
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 2 distinct chains · 46% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Heat shock protein 104	protein	579	48% helix, 11% strand	P31539
P	Alpha-S1-casein	protein	28	0% helix, 14% strand	—

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 12 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	571	0.87	0.93	77	AGS
2	626	0.86	0.91	80	AGS
3	918	0.86	0.88	117	empty
4	519	0.86	0.92	74	AGS
5	566	0.85	0.91	73	empty

Interfaces

18 interfaces between chains.

C–D · 4629 Å² buried · 67 hydrogen bonds · protein-protein
E–F · 4581 Å² buried · 75 hydrogen bonds · protein-protein
B–C · 4433 Å² buried · 72 hydrogen bonds · protein-protein
D–E · 4416 Å² buried · 57 hydrogen bonds · protein-protein
A–B · 4208 Å² buried · 74 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 covalent, 2 disulfide (covalent ligand, disulfide).

Compared structures

5VYA · S. cerevisiae Hsp104:casein complex, Extended Conformation · the same entry in another collection · chain P against P, TM-score 1.00
P31539 · AlphaFold monomer V2.0 prediction for heat shock protein 104 (P31539) · a predicted model of the same protein · chain A against A, TM-score 0.90

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 P31539
Elsewhere: RCSB PDB 5VYA · PDBe 5VYA · UniProt P31539

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