MolNFT v1 · #124717 · protein

Cryoem reconstruction of HSP104 hexamer

5KNE · Heat shock protein 104: “Cryoem reconstruction of HSP104 hexamer”. Electron microscopy, 1 ligand (ANP), 20 pockets (best druggability 0.69). MolNFT v1 #124717 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5KNE
Type: protein
Length: 4,020 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat shock protein 104
UniProt: P31539
Ligands: ANP
Pockets: 20 · best druggability 0.69

Structure

electron microscopy · 6 distinct chains · 50% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heat shock protein 104	protein	553	49% helix, 9% strand	P31539
B	Heat shock protein 104	protein	711	47% helix, 8% strand	P31539
C	Heat shock protein 104	protein	769	49% helix, 6% strand	P31539
D	Heat shock protein 104	protein	770	49% helix, 6% strand	P31539
E	Heat shock protein 104	protein	610	54% helix, 7% strand	P31539
F	Heat shock protein 104	protein	607	50% helix, 9% strand	P31539

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · 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	1042	0.69	0.75	116	empty
2	998	0.68	0.74	127	empty
3	1056	0.68	0.74	144	empty
4	1114	0.68	0.74	137	empty
5	926	0.67	0.74	99	empty

Interfaces

6 interfaces between chains.

B–C · 285 Å² buried · 1 hydrogen bond · protein-protein
C–D · 273 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 222 Å² buried · 0 hydrogen bonds · protein-protein
E–F · 203 Å² buried · 1 hydrogen bond · protein-protein
D–E · 190 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5KNE · CryoEM Reconstruction of Hsp104 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 A 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 5KNE · PDBe 5KNE · UniProt P31539

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