MolNFT v1 · #170955 · protein
Product bound structure of the ectoine utilization protein eutd (doea) from halomonas elongata
6YO9 · Ectoine hydrolase doea: “Product bound structure of the ectoine utilization protein eutd (doea) from halomonas elongata”. X-ray diffraction, 1 ligand (P4B), 8 pockets (best druggability 0.82). MolNFT v1 #170955 on GenesisL1: 3D…
- PDB
- 6YO9
- Type
- protein
- Length
- 794 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectoine hydrolase doea
- EC
- 3.4.-.-
- UniProt
- A0A1B8NWR1
- Ligands
- P4B
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ectoine hydrolase doea (EC 3.4.-.-) | protein | 396 | 36% helix, 21% strand | A0A1B8NWR1 |
| A | Ectoine hydrolase doea (EC 3.4.-.-) | protein | 398 | 37% helix, 22% strand | A0A1B8NWR1 |
Ligands and binding sites
- P4B · (2~{R})-4-azanyl-2-[[(1~{S})-1-oxidanylethyl]amino]butanoic acid · ligand · 2 copies · chains B, A
- GOL · Glycerol · additive · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.82 | 0.84 | 78 | P4B |
| 2 | 58 | 0.73 | 0.99 | 20 | P4B |
| 3 | 295 | 0.71 | 0.85 | 37 | GOL |
| 4 | 413 | 0.69 | 0.81 | 46 | empty |
| 5 | 148 | 0.65 | 0.87 | 33 | empty |
Interfaces
1 interface between chains.
- B–A · 2968 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 6YO9 · Product bound structure of the Ectoine utilization protein EutD (DoeA) from Halomonas… · the same entry in another collection · chain B against B, 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 A0A1B8NWR1
- Elsewhere: RCSB PDB 6YO9 · PDBe 6YO9 · UniProt A0A1B8NWR1
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