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Complex of yeast cytoplasmic dynein MTBD-High and MT without DTT

Analyse Complex of yeast cytoplasmic dynein MTBD-High and MT without DTT in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KIO
Type: protein
Length: 968 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.94
Source: Saccharomyces cerevisiae S288c; Sus scrofa
Molecule: Tubulin beta chain; Dynein heavy chain, cytoplasmic; Tubulin alpha-1A chain
UniProt: P02554, P36022
Pockets: 14 · best druggability 0.81

Structure

electron microscopy · resolution 3.94 · 3 distinct chains · 47% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
b	Tubulin beta chain	protein	426	45% helix, 15% strand	P02554
M	Dynein heavy chain, cytoplasmic	protein	130	61% helix, 0% strand	P36022
a	Tubulin alpha-1A chain	protein	412	46% helix, 16% strand	—

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	222	0.81	0.95	44	empty
2	591	0.77	0.83	76	empty
3	60	0.68	0.96	20	empty
4	69	0.61	0.91	22	empty
5	226	0.54	0.78	28	empty

Interfaces

3 interfaces between chains.

b–a · 1739 Å² buried · 23 hydrogen bonds · protein-protein
M–a · 590 Å² buried · 17 hydrogen bonds · protein-protein
b–M · 558 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6KIO · Complex of yeast cytoplasmic dynein mtbd-high and mt without dtt · the same entry in another collection · chain M against M, TM-score 1.00
P02554 · AlphaFold monomer V2.0 prediction for tubulin beta chain (P02554) · a predicted model of the same protein · chain b against A, TM-score 0.97

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 P02554
Every structure of UniProt P36022
Elsewhere: RCSB PDB 6KIO · PDBe 6KIO · UniProt P02554 · UniProt P36022

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