Research workbench
Cryo-EM structure of yeast cytoplasmic dynein with walker B mutation at AAA3 in presence of ATP-VO4
Analyse Cryo-EM structure of yeast cytoplasmic dynein with walker B mutation at AAA3 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VLJ
- Type
- protein
- Length
- 3,084 residues
- Chains
- 3
- 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 0.86
Structure
electron microscopy · 2 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynein heavy chain, cytoplasmic | protein | 2376 | 52% helix, 9% strand | P36022 |
| B, C | Nuclear distribution protein PAC1 | protein | 354 | 6% helix, 45% 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 | 1055 | 0.86 | 0.87 | 106 | empty |
| 2 | 1055 | 0.84 | 0.85 | 74 | empty |
| 3 | 705 | 0.83 | 0.86 | 82 | empty |
| 4 | 123 | 0.82 | 0.99 | 26 | empty |
| 5 | 256 | 0.81 | 0.92 | 54 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1094 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 781 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 516 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5VLJ · Cryo-EM structure of yeast cytoplasmic dynein with Walker B mutation at AAA3 in presence… · 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 0.90
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 5VLJ · PDBe 5VLJ · UniProt P36022 · UniProt A6ZPA6
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