Research workbench
A novel metagenomic ALPHA/BETA-fold esterase
Analyse A novel metagenomic ALPHA/BETA-fold esterase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z69
- Type
- protein
- Length
- 721 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl ESTERASE/LIPASE
- UniProt
- A0A1M6Y2K1
- Ligands
- HEE, 4MU, MG
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl ESTERASE/LIPASE | protein | 357 | 43% helix, 16% strand | A0A1M6Y2K1 |
| B | Acetyl ESTERASE/LIPASE | protein | 364 | 42% helix, 16% strand | A0A1M6Y2K1 |
Ligands and binding sites
- HEE · N-hexylphosphonate ethyl ester · ligand · 3 copies · chains A, B
- 4MU · 7-hydroxy-4-methyl-2H-chromen-2-one · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.79 | 0.97 | 23 | HEE |
| 2 | 253 | 0.77 | 0.90 | 40 | HEE, 4MU |
| 3 | 463 | 0.63 | 0.76 | 51 | empty |
| 4 | 108 | 0.44 | 0.78 | 19 | empty |
| 5 | 90 | 0.39 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 927 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6Z69 · A novel metagenomic alpha/beta-fold esterase · 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 A0A1M6Y2K1
- Elsewhere: RCSB PDB 6Z69 · PDBe 6Z69 · UniProt A0A1M6Y2K1
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