Research workbench

ADP-bound human mitochondrial Hsp60-Hsp10 half-football complex

Analyse ADP-bound human mitochondrial Hsp60-Hsp10 half-football complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MRD
Type: protein
Length: 4,396 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.82
Source: Homo sapiens
Molecule: 60 kDa heat shock protein, mitochondrial; 10 kDa heat shock protein, mitochondrial
EC: 3.6.4.9
UniProt: P10809, P61604
Ligands: ADP, MG
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · resolution 3.82 · 2 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, F, E, D, C, B	60 kDa heat shock protein, mitochondrial (EC 3.6.4.9)	protein	528	50% helix, 15% strand	P10809
O, U, T, S, R, Q, P	10 kDa heat shock protein, mitochondrial	protein	100	3% helix, 39% strand	P61604

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 7 copies · chains A, G, F, E, D, C, B
MG · Magnesium ion · metal · 7 copies · chains A, G, F, E, D, C, B

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	586	0.83	0.88	65	ADP, MG
2	587	0.82	0.88	63	ADP, MG
3	594	0.82	0.87	62	ADP, MG
4	595	0.82	0.87	63	ADP, MG
5	592	0.82	0.87	64	ADP, MG

Interfaces

28 interfaces between chains.

C–B · 1966 Å² buried · 22 hydrogen bonds · protein-protein
A–G · 1953 Å² buried · 21 hydrogen bonds · protein-protein
E–D · 1942 Å² buried · 21 hydrogen bonds · protein-protein
F–E · 1938 Å² buried · 21 hydrogen bonds · protein-protein
G–F · 1931 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

6MRD · ADP-bound human mitochondrial HSP60-HSP10 half-football complex · the same entry in another collection · chain Q against Q, TM-score 1.00

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 P10809
Every structure of UniProt P61604
Elsewhere: RCSB PDB 6MRD · PDBe 6MRD · UniProt P10809 · UniProt P61604

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