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Orthorhombic crystal structure of an acetylester hydrolase from corynebacterium glutamicum
Analyse Orthorhombic crystal structure of an acetylester hydrolase from corynebacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D6O
- Type
- protein
- Length
- 1,396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoserine O-acetyltransferase
- EC
- 2.3.1.-, 2.3.1.31
- UniProt
- Q8NS43
- Ligands
- MG, CL
- Pockets
- 18 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Homoserine O-acetyltransferase (EC 2.3.1.-, 2.3.1.31) | protein | 349 | 47% helix, 14% strand | Q8NS43 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 17 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.57 | 0.80 | 20 | empty |
| 2 | 221 | 0.56 | 0.79 | 20 | empty |
| 3 | 237 | 0.55 | 0.78 | 31 | empty |
| 4 | 141 | 0.48 | 0.77 | 21 | CL |
| 5 | 118 | 0.47 | 0.79 | 17 | CL, GOL |
Interfaces
3 interfaces between chains.
- A–B · 1464 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1447 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 233 Ų buried · 0 hydrogen bonds · protein-protein
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 Q8NS43
- Elsewhere: RCSB PDB 5D6O · PDBe 5D6O · UniProt Q8NS43
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