Research workbench
Crystal structure of ectd from S. alaskensis with 2-oxoglutarate and 5-hydroxyectoine
Analyse Crystal structure of ectd from S. alaskensis with 2-oxoglutarate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q5O
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectoine hydroxylase
- UniProt
- Q1GNW5
- Ligands
- AKG, 6CS, FE
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ectoine hydroxylase | protein | 282 | 26% helix, 24% strand | Q1GNW5 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- 6CS · (4S,5S)-5-hydroxy-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.75 | 0.85 | 56 | FE, AKG, 6CS |
| 2 | 265 | 0.61 | 0.80 | 36 | FE, AKG, 6CS |
| 3 | 51 | 0.26 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1080 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4Q5O · Crystal structure of EctD from S. alaskensis with 2-oxoglutarate and 5-hydroxyectoine · the same entry in another collection · chain A against A, TM-score 1.00
- Q1GNW5 · AlphaFold monomer V2.0 prediction for ectoine dioxygenase (Q1GNW5) · a predicted model of the same protein · chain A 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 Q1GNW5
- Elsewhere: RCSB PDB 4Q5O · PDBe 4Q5O · UniProt Q1GNW5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.