Research workbench
Monoclinic structure of the acetyl esterase mekb
Analyse Monoclinic structure of the acetyl esterase mekb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EFZ
- Type
- protein
- Length
- 2,068 residues
- Chains
- 6
- 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
- Q0MRG5
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Homoserine O-acetyltransferase (EC 2.3.1.-, 2.3.1.31) | protein | 347 | 46% helix, 14% strand | Q0MRG5 |
| B, E | Homoserine O-acetyltransferase (EC 2.3.1.-, 2.3.1.31) | protein | 345 | 47% helix, 14% strand | Q0MRG5 |
| C | Homoserine O-acetyltransferase (EC 2.3.1.-, 2.3.1.31) | protein | 339 | 46% helix, 15% strand | Q0MRG5 |
| D | Homoserine O-acetyltransferase (EC 2.3.1.-, 2.3.1.31) | protein | 345 | 46% helix, 14% strand | Q0MRG5 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 25 copies · chains A, B, C, D, F, E
- GOL · Glycerol · additive · 8 copies · chains A, C, D, F
- ACT · Acetate ion · additive · 7 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.78 | 0.80 | 82 | EDO |
| 2 | 417 | 0.73 | 0.84 | 54 | EDO, GOL |
| 3 | 83 | 0.70 | 0.94 | 14 | GOL |
| 4 | 63 | 0.70 | 0.96 | 14 | ACT |
| 5 | 113 | 0.67 | 0.89 | 17 | empty |
Interfaces
7 interfaces between chains.
- C–E · 1388 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1353 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1353 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 490 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 286 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5EFZ · Monoclinic structure of the acetyl esterase MekB · the same entry in another collection · chain A against A, 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 Q0MRG5
- Elsewhere: RCSB PDB 5EFZ · PDBe 5EFZ · UniProt Q0MRG5
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