Research workbench

HSP104DWB extended conformation

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

PDB: 6N8Z
Type: protein
Length: 4,050 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 0.88

Structure

electron microscopy · 2 distinct chains · 49% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Heat shock protein 104	protein	579	48% helix, 11% strand	P31539
B, C, D, E	Heat shock protein 104	protein	723	50% helix, 11% strand	P31539

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · 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	1031	0.88	0.89	128	ATP
2	992	0.87	0.89	116	ATP
3	826	0.87	0.90	95	ATP
4	619	0.86	0.91	89	ATP
5	710	0.85	0.88	92	ATP

Interfaces

13 interfaces between chains.

B–C · 4137 Å² buried · 63 hydrogen bonds · protein-protein
C–D · 4124 Å² buried · 66 hydrogen bonds · protein-protein
D–E · 3992 Å² buried · 38 hydrogen bonds · protein-protein
E–F · 3222 Å² buried · 45 hydrogen bonds · protein-protein
A–B · 2141 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 covalent, 2 disulfide (covalent ligand, disulfide).

Compared structures

6N8Z · HSP104DWB extended 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 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 6N8Z · PDBe 6N8Z · UniProt P31539

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