MolNFT v1 · #157739 · protein

HSP104DWB closed conformation

6N8T · Heat shock protein 104: “HSP104DWB closed conformation”. Electron microscopy, 1 ligand (ATP), 20 pockets (best druggability 0.89). MolNFT v1 #157739 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6N8T
Type: protein
Length: 4,702 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat shock protein 104
UniProt: P31539
Ligands: ATP
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 3 distinct chains · 50% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F	Heat shock protein 104	protein	848	54% helix, 8% strand	P31539
C, E	Heat shock protein 104	protein	719	48% helix, 9% strand	P31539
D	Heat shock protein 104	protein	720	49% helix, 9% strand	P31539

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 12 copies · chains A, F, B, C, D, E

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	1162	0.89	0.91	168	ATP
2	879	0.88	0.90	116	ATP
3	1031	0.86	0.88	120	ATP
4	487	0.86	0.93	80	empty
5	606	0.84	0.89	65	ATP

Interfaces

10 interfaces between chains.

D–E · 4312 Å² buried · 58 hydrogen bonds · protein-protein
B–C · 4041 Å² buried · 54 hydrogen bonds · protein-protein
C–D · 3880 Å² buried · 56 hydrogen bonds · protein-protein
A–B · 3398 Å² buried · 45 hydrogen bonds · protein-protein
A–F · 3027 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

6N8T · Hsp104DWB closed conformation · 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 D against A, TM-score 0.85

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 6N8T · PDBe 6N8T · UniProt P31539

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