MolNFT v1 · #128559 · protein
Motor domains from human cytoplasmic dynein-1 in the phi-particle conformation
5NUG · Cytoplasmic dynein 1 heavy chain 1: “Motor domains from human cytoplasmic dynein-1 in the phi-particle conformation”. Electron microscopy, 3 ligands (ADP, ATP, MG), 20 pockets (best druggability 0.84). MolNFT v1 #128559 on…
- PDB
- 5NUG
- Type
- protein
- Length
- 5,840 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytoplasmic dynein 1 heavy chain 1
- UniProt
- Q14204
- Ligands
- ADP, ATP, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytoplasmic dynein 1 heavy chain 1 | protein | 2920 | 56% helix, 10% strand | Q14204 |
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 | 809 | 0.84 | 0.87 | 101 | ADP |
| 2 | 1120 | 0.83 | 0.84 | 107 | ADP |
| 3 | 1162 | 0.83 | 0.84 | 119 | ADP |
| 4 | 1154 | 0.82 | 0.84 | 127 | ADP |
| 5 | 1169 | 0.79 | 0.81 | 107 | empty |
Interfaces
1 interface between chains.
- A–B · 1895 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5NUG · Motor domains from human cytoplasmic dynein-1 in the phi-particle conformation · 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 Q14204
- Elsewhere: RCSB PDB 5NUG · PDBe 5NUG · UniProt Q14204
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