MolNFT v1 · #152130 · protein
Structure of ester-hydrolase EH1AB1 from the metagenome of lake arreo complexed with a derivative of butyl 4-nitrophenyl hexylphosphonate
6I8D: “Structure of ester-hydrolase EH1AB1 from the metagenome of lake arreo complexed with a derivative of butyl…”. X-ray diffraction, 1 ligand (H7N), 5 pockets (best druggability 0.81). MolNFT v1 #152130 on GenesisL1: 3D structure…
- PDB
- 6I8D
- Type
- protein
- Length
- 630 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EH1AB1
- Ligands
- H7N
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | EH1AB1 | protein | 315 | 42% helix, 20% strand | — |
Ligands and binding sites
- H7N · butoxy(hexyl)phosphinic acid · ligand · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.81 | 0.84 | 73 | H7N |
| 2 | 667 | 0.80 | 0.85 | 66 | H7N, GOL |
| 3 | 73 | 0.44 | 0.82 | 18 | empty |
| 4 | 75 | 0.29 | 0.72 | 14 | empty |
| 5 | 78 | 0.29 | 0.72 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1045 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6I8D · Structure of ester-hydrolase EH1AB1 from the metagenome of lake arreo complexed with a… · 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
- Elsewhere: RCSB PDB 6I8D · PDBe 6I8D
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