Research workbench

Cryoem reconstruction of HSP104 N728A hexamer

Analyse Cryoem reconstruction of HSP104 N728A hexamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AHF
Type: protein
Length: 4,323 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat shock protein 104
UniProt: P31539
Ligands: AGS
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 5 distinct chains · 43% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heat shock protein 104	protein	577	40% helix, 1% strand	P31539
B	Heat shock protein 104	protein	737	37% helix, 2% strand	P31539
C, D	Heat shock protein 104	protein	865	45% helix, 1% strand	P31539
E	Heat shock protein 104	protein	705	52% helix, 0% strand	P31539
F	Heat shock protein 104	protein	574	42% helix, 1% strand	P31539

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 6 copies · chains 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	905	0.89	0.91	141	empty
2	937	0.88	0.89	128	empty
3	652	0.87	0.91	93	empty
4	613	0.87	0.91	89	empty
5	623	0.87	0.91	85	empty

Interfaces

6 interfaces between chains.

C–D · 1900 Å² buried · 33 hydrogen bonds · protein-protein
D–E · 1733 Å² buried · 33 hydrogen bonds · protein-protein
B–C · 1483 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1367 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 1349 Å² buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent, 1 isopeptide (covalent ligand, isopeptide).

Compared structures

6AHF · CryoEM Reconstruction of Hsp104 N728A Hexamer · 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 F against A, TM-score 0.84

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 6AHF · PDBe 6AHF · UniProt P31539

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.