Research workbench

Dynein motor domain - ATP complex

Analyse Dynein motor domain - ATP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4AKG
Type: protein
Length: 5,300 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutathione S-transferase class-mu 26 kda isozyme, dynein heavy chain cytoplasmic
EC: 2.5.1.18
UniProt: P08515, P36022
Ligands: ATP, ADP, MG, SO4
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glutathione S-transferase class-mu 26 kda isozyme, dynein heavy chain cytoplasmic (EC 2.5.1.18)	protein	2650	56% helix, 10% strand	P08515, P36022

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, 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	988	0.85	0.86	123	ADP
2	997	0.85	0.86	134	ADP
3	814	0.81	0.84	74	SO4
4	1100	0.80	0.82	97	SO4
5	553	0.79	0.85	63	empty

Interfaces

1 interface between chains.

A–B · 30 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4AKG · Dynein Motor Domain - ATP complex · the same entry in another collection · chain A against A, TM-score 1.00
P08515 · AlphaFold monomer V2.0 prediction for glutathione S-transferase class-mu 26 kda isozyme… · a predicted model of the same protein · chain A against A, TM-score 0.08

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 P08515
Every structure of UniProt P36022
Elsewhere: RCSB PDB 4AKG · PDBe 4AKG · UniProt P08515 · UniProt P36022

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