Research workbench
Structure of ester-hydrolase EH3 from the metagenome of marine sediments at milazzo harbor (sicily, italy) complexed with a derivative of butyl 4-nitrophenyl hexylphosphonate
Analyse Structure of ester-hydrolase EH3 from the metagenome of marine sediments at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SYL
- Type
- protein
- Length
- 679 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Esterase
- UniProt
- A0A2K8JN75
- Ligands
- H7N
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Esterase | protein | 339 | 38% helix, 19% strand | A0A2K8JN75 |
| B | Esterase | protein | 340 | 37% helix, 19% strand | A0A2K8JN75 |
Ligands and binding sites
- H7N · butoxy(hexyl)phosphinic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.84 | 0.91 | 43 | H7N |
| 2 | 382 | 0.81 | 0.89 | 56 | H7N |
| 3 | 429 | 0.61 | 0.76 | 68 | empty |
| 4 | 192 | 0.46 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1063 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6SYL · Structure of ester-hydrolase EH3 from the metagenome of marine sediments at milazzo… · 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 A0A2K8JN75
- Elsewhere: RCSB PDB 6SYL · PDBe 6SYL · UniProt A0A2K8JN75
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