MolNFT v1 · #165472 · protein
Product bound structure of the ectoine utilization protein eute (doeb) from ruegeria pomeroyi
6TWM · N-acetyl-L-2,4-diaminobutyric acid deacetylase: “Product bound structure of the ectoine utilization protein eute (doeb) from ruegeria pomeroyi”. X-ray diffraction, 2 ligands (DAB, ZN), 20 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 6TWM
- Type
- protein
- Length
- 3,916 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetyl-L-2,4-diaminobutyric acid deacetylase
- UniProt
- Q5LUB5
- Ligands
- DAB, ZN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, I | N-acetyl-L-2,4-diaminobutyric acid deacetylase | protein | 326 | 25% helix, 31% strand | Q5LUB5 |
| C | N-acetyl-L-2,4-diaminobutyric acid deacetylase | protein | 325 | 24% helix, 29% strand | Q5LUB5 |
| D | N-acetyl-L-2,4-diaminobutyric acid deacetylase | protein | 328 | 24% helix, 31% strand | Q5LUB5 |
| E, G, H, K | N-acetyl-L-2,4-diaminobutyric acid deacetylase | protein | 327 | 24% helix, 31% strand | Q5LUB5 |
| F | N-acetyl-L-2,4-diaminobutyric acid deacetylase | protein | 327 | 24% helix, 30% strand | Q5LUB5 |
| J | N-acetyl-L-2,4-diaminobutyric acid deacetylase | protein | 326 | 25% helix, 30% strand | Q5LUB5 |
| L | N-acetyl-L-2,4-diaminobutyric acid deacetylase | protein | 324 | 25% helix, 30% strand | Q5LUB5 |
Ligands and binding sites
- DAB · 2,4-diaminobutyric acid · ligand · 7 copies · chains A, K, B, D, G, E, F, J
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, D, E, G, H, I, J, L
- ACT · Acetate ion · additive · 3 copies · chains C, G, J, H
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 | 975 | 0.81 | 0.82 | 112 | ZN, DAB |
| 2 | 1134 | 0.77 | 0.79 | 82 | empty |
| 3 | 518 | 0.77 | 0.85 | 57 | DAB |
| 4 | 1107 | 0.77 | 0.79 | 96 | empty |
| 5 | 666 | 0.77 | 0.82 | 68 | ACT |
Interfaces
30 interfaces between chains.
- A–G · 1905 Ų buried · 25 hydrogen bonds · protein-protein
- F–J · 1900 Ų buried · 24 hydrogen bonds · protein-protein
- C–L · 1865 Ų buried · 22 hydrogen bonds · protein-protein
- B–H · 1852 Ų buried · 23 hydrogen bonds · protein-protein
- D–K · 1850 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6TWM · Product bound structure of the Ectoine utilization protein EutE (DoeB) from Ruegeria… · the same entry in another collection · chain F against F, 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 Q5LUB5
- Elsewhere: RCSB PDB 6TWM · PDBe 6TWM · UniProt Q5LUB5
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