MolNFT v1 · #137200 · protein
Cryo-EM structure of yeast cytoplasmic dynein-1 with LIS1 and ATP
5VH9 · Dynein heavy chain, cytoplasmic: “Cryo-EM structure of yeast cytoplasmic dynein-1 with LIS1 and ATP”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #137200 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5VH9
- Type
- protein
- Length
- 2,730 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynein heavy chain, cytoplasmic; Nuclear distribution protein PAC1
- UniProt
- P36022, A6ZPA6
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynein heavy chain, cytoplasmic | protein | 2376 | 53% helix, 10% strand | P36022 |
| B | Nuclear distribution protein PAC1 | protein | 354 | 6% helix, 44% strand | A6ZPA6 |
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 | 1018 | 0.87 | 0.88 | 143 | empty |
| 2 | 554 | 0.85 | 0.90 | 68 | empty |
| 3 | 494 | 0.84 | 0.90 | 70 | empty |
| 4 | 843 | 0.84 | 0.86 | 92 | empty |
| 5 | 476 | 0.80 | 0.87 | 60 | empty |
Interfaces
1 interface between chains.
- A–B · 289 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5VH9 · Cryo-EM structure of yeast cytoplasmic dynein-1 with Lis1 and ATP · the same entry in another collection · chain A against A, TM-score 1.00
- A6ZPA6 · AlphaFold monomer V2.0 prediction for nuclear distribution protein PAC1 (A6ZPA6) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P36022
- Every structure of UniProt A6ZPA6
- Elsewhere: RCSB PDB 5VH9 · PDBe 5VH9 · UniProt P36022 · UniProt A6ZPA6
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