MolNFT v1 · #129850 · protein
Human cytoplasmic dynein N-terminus dimerization domain at 1.8 ångström resolution
5OWO · Cytoplasmic dynein 1 heavy chain 1: “Human cytoplasmic dynein N-terminus dimerization domain at 1.8 ångström resolution”. X-ray diffraction, 4 ligands (MG, CA, NA), 10 pockets (best druggability 0.51). MolNFT v1 #129850 on…
- PDB
- 5OWO
- Type
- protein
- Length
- 637 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytoplasmic dynein 1 heavy chain 1
- UniProt
- Q14204
- Ligands
- MG, CA, NA, K
- Pockets
- 10 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytoplasmic dynein 1 heavy chain 1 | protein | 162 | 50% helix, 21% strand | Q14204 |
| B | Cytoplasmic dynein 1 heavy chain 1 | protein | 158 | 51% helix, 20% strand | Q14204 |
| C | Cytoplasmic dynein 1 heavy chain 1 | protein | 160 | 51% helix, 20% strand | Q14204 |
| D | Cytoplasmic dynein 1 heavy chain 1 | protein | 157 | 50% helix, 20% strand | Q14204 |
Ligands and binding sites
- MG · Magnesium ion · metal · 26 copies · chains A, C, D, B
- CA · Calcium ion · metal · 2 copies · chains A, C, D
- NA · Sodium ion · metal · chains B
- K · Potassium ion · metal · chains D
- GOL · Glycerol · additive · 9 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.51 | 0.83 | 20 | empty |
| 2 | 130 | 0.49 | 0.79 | 21 | empty |
| 3 | 94 | 0.48 | 0.82 | 21 | MG |
| 4 | 102 | 0.48 | 0.81 | 22 | MG |
| 5 | 68 | 0.47 | 0.84 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2732 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 2709 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 693 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
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 5OWO · PDBe 5OWO · UniProt Q14204
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