Research workbench
Cryo-EM structure of mouse cytoplasmic dynein-1 microtubule binding domain bound to microtubules
Analyse Cryo-EM structure of mouse cytoplasmic dynein-1 microtubule binding domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RZB
- Type
- protein
- Length
- 1,001 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain; MKIAA0325 protein
- UniProt
- Q2XVP4, P02554, Q80U36
- Ligands
- GTP, GDP, TA1, MG
- Pockets
- 9 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 426 | 43% helix, 17% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 426 | 47% helix, 19% strand | P02554 |
| C | MKIAA0325 protein | protein | 149 | 67% helix, 0% strand | Q80U36 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- TA1 · Taxol · ligand · chains B
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.81 | 0.96 | 40 | GTP, MG |
| 2 | 206 | 0.66 | 0.85 | 40 | empty |
| 3 | 298 | 0.66 | 0.81 | 40 | empty |
| 4 | 296 | 0.59 | 0.78 | 27 | TA1 |
| 5 | 197 | 0.59 | 0.81 | 35 | GDP |
Interfaces
3 interfaces between chains.
- A–B · 1983 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 577 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 509 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6RZB · Cryo-EM structure of mouse cytoplasmic dynein-1 microtubule binding domain bound to… · 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 Q2XVP4
- Every structure of UniProt P02554
- Every structure of UniProt Q80U36
- Elsewhere: RCSB PDB 6RZB · PDBe 6RZB · UniProt Q2XVP4 · UniProt P02554 · UniProt Q80U36
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