MolNFT v1 · #137753 · protein

S. cerevisiae HSP104-ADP complex

5VY8 · Heat shock protein 104: “S. cerevisiae HSP104-ADP complex”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.84). MolNFT v1 #137753 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VY8
Type: protein
Length: 3,846 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat shock protein 104
UniProt: P31539
Ligands: ADP
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 2 distinct chains · 53% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F	Heat shock protein 104	protein	577	48% helix, 11% strand	P31539
C, D, E	Heat shock protein 104	protein	705	56% helix, 9% strand	P31539

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · 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	1116	0.84	0.85	114	ADP
2	1016	0.83	0.84	115	ADP
3	837	0.83	0.85	91	ADP
4	930	0.82	0.83	82	ADP
5	1193	0.81	0.83	111	ADP

Interfaces

6 interfaces between chains.

C–D · 2544 Å² buried · 33 hydrogen bonds · protein-protein
D–E · 2523 Å² buried · 34 hydrogen bonds · protein-protein
A–B · 2069 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1945 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 1823 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

5VY8 · S. cerevisiae Hsp104-ADP complex · the same entry in another collection · chain F against F, TM-score 1.00
P31539 · AlphaFold monomer V2.0 prediction for heat shock protein 104 (P31539) · a predicted model of the same protein · chain C against A, TM-score 0.82

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 5VY8 · PDBe 5VY8 · UniProt P31539

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