Research workbench
Pseudo-atomic model of dynein microtubule binding domain-tubulin complex based on a cryoem MAP
Analyse Pseudo-atomic model of dynein microtubule binding domain-tubulin complex based… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J6P
- Type
- protein
- Length
- 946 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynein heavy chain, cytoplasmic; Tubulin alpha-1A chain; Tubulin beta chain
- UniProt
- P34036, P02550, P02554
- Ligands
- GTP, GDP, TA1, MG
- Pockets
- 16 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Dynein heavy chain, cytoplasmic | protein | 108 | 63% helix, 0% strand | P34036 |
| A | Tubulin alpha-1A chain | protein | 412 | 46% helix, 16% strand | P02550 |
| B | Tubulin beta chain | protein | 426 | 48% helix, 15% strand | P02554 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.83 | 0.84 | 104 | empty |
| 2 | 221 | 0.82 | 0.96 | 42 | MG, GTP |
| 3 | 84 | 0.74 | 0.97 | 22 | empty |
| 4 | 69 | 0.70 | 0.96 | 25 | empty |
| 5 | 391 | 0.61 | 0.76 | 45 | TA1 |
Interfaces
3 interfaces between chains.
- A–B · 1868 Ų buried · 29 hydrogen bonds · protein-protein
- D–B · 633 Ų buried · 10 hydrogen bonds · protein-protein
- D–A · 355 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3J6P · Pseudo-atomic model of dynein microtubule binding domain-tubulin complex based on a… · the same entry in another collection · chain D against D, TM-score 1.00
- P02550 · AlphaFold monomer V2.0 prediction for tubulin alpha-1A chain (P02550) · a predicted model of the same protein · chain A 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 P34036
- Every structure of UniProt P02550
- Every structure of UniProt P02554
- Elsewhere: RCSB PDB 3J6P · PDBe 3J6P · UniProt P34036 · UniProt P02550 · UniProt P02554
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