MolNFT v1 · #127532 · protein
Crystal structure of ODA16 from chlamydomonas reinhardtii
5MZH · Dynein assembly factor with wdr repeat domains 1: “Crystal structure of ODA16 from chlamydomonas reinhardtii”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.81). MolNFT v1 #127532 on GenesisL1: 3D structure…
- PDB
- 5MZH
- Type
- protein
- Length
- 825 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynein assembly factor with wdr repeat domains 1
- UniProt
- Q3Y8L7
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynein assembly factor with wdr repeat domains 1 | protein | 410 | 7% helix, 48% strand | Q3Y8L7 |
| B | Dynein assembly factor with wdr repeat domains 1 | protein | 415 | 7% helix, 49% strand | Q3Y8L7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.81 | 0.83 | 58 | empty |
| 2 | 1163 | 0.80 | 0.81 | 62 | empty |
| 3 | 373 | 0.69 | 0.82 | 48 | empty |
| 4 | 359 | 0.62 | 0.78 | 40 | empty |
| 5 | 122 | 0.52 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 710 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5MZH · Crystal structure of ODA16 from Chlamydomonas reinhardtii · the same entry in another collection · chain A against A, TM-score 1.00
- Q3Y8L7 · AlphaFold monomer V2.0 prediction for dynein assembly factor with wdr repeat domains 1… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q3Y8L7
- Elsewhere: RCSB PDB 5MZH · PDBe 5MZH · UniProt Q3Y8L7
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