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