Research workbench
Product bound structure of the ectoine utilization protein eutd (doea) from halomonas elongata
Analyse Product bound structure of the ectoine utilization protein eutd (doea) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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