Research workbench
Structure of the dynein-2 complex; motor domains
Analyse Structure of the dynein-2 complex; motor domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RLA
- Type
- protein
- Length
- 5,500 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O6-alkylguanine-DNA alkyltransferase MUTANT,DYNC2H1 variant protein
- UniProt
- E5BBQ0, B0I1S0
- Ligands
- ADP, ATP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O6-alkylguanine-DNA alkyltransferase MUTANT,DYNC2H1 variant protein | protein | 2750 | 51% helix, 10% strand | E5BBQ0, B0I1S0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.86 | 0.88 | 107 | ADP |
| 2 | 741 | 0.86 | 0.89 | 102 | ADP |
| 3 | 619 | 0.85 | 0.90 | 82 | empty |
| 4 | 947 | 0.85 | 0.86 | 120 | empty |
| 5 | 1187 | 0.84 | 0.85 | 110 | empty |
Interfaces
1 interface between chains.
- A–B · 1461 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6RLA · Structure of the dynein-2 complex; motor domains · the same entry in another collection · chain A against A, 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 E5BBQ0
- Every structure of UniProt B0I1S0
- Elsewhere: RCSB PDB 6RLA · PDBe 6RLA · UniProt E5BBQ0 · UniProt B0I1S0
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