Research workbench

HSP104DWB open conformation

Analyse HSP104DWB open conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6N8V
Type: protein
Length: 4,315 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 0.69

Structure

electron microscopy · 6 distinct chains · 48% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heat shock protein 104	protein	704	47% helix, 8% strand	P31539
B	Heat shock protein 104	protein	710	47% helix, 8% strand	P31539
C	Heat shock protein 104	protein	713	48% helix, 6% strand	P31539
D	Heat shock protein 104	protein	769	49% helix, 6% strand	P31539
E	Heat shock protein 104	protein	709	48% helix, 6% strand	P31539
F	Heat shock protein 104	protein	710	46% helix, 8% strand	P31539

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 11 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	965	0.69	0.75	121	empty
2	1054	0.69	0.74	141	empty
3	949	0.68	0.75	108	empty
4	1175	0.67	0.74	154	empty
5	928	0.67	0.74	116	empty

Interfaces

6 interfaces between chains.

A–B · 331 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 273 Å² buried · 1 hydrogen bond · protein-protein
C–D · 272 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 267 Å² buried · 1 hydrogen bond · protein-protein
D–E · 191 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6N8V · Hsp104DWB open 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 E against A, TM-score 0.79

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 6N8V · PDBe 6N8V · UniProt P31539

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