MolNFT v1 · #147377 · protein
Structural and enzymatic characterization of an esterase from a metagenomic library
6EB3 · EST1: “Structural and enzymatic characterization of an esterase from a metagenomic library”. X-ray diffraction, 5 ligands (ABU, J3J, J3G), 12 pockets (best druggability 0.87). MolNFT v1 #147377 on GenesisL1: 3D structure, binding…
- PDB
- 6EB3
- Type
- protein
- Length
- 1,063 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EST1
- Ligands
- ABU, J3J, J3G, SO4, PO4
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EST1 | protein | 265 | 43% helix, 18% strand | — |
| B, D | EST1 | protein | 268 | 47% helix, 18% strand | — |
| C | EST1 | protein | 262 | 44% helix, 19% strand | — |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · 2 copies · chains C, D
- J3J · 1,3-dihydroxypropan-2-yl butanoate · ligand · chains A
- J3G · 2-hydroxypropane-1,3-diyl dibutanoate · ligand · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains C, D
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 4 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.87 | 0.88 | 85 | ABU, EDO |
| 2 | 773 | 0.85 | 0.88 | 74 | empty |
| 3 | 834 | 0.85 | 0.87 | 70 | GOL |
| 4 | 708 | 0.85 | 0.88 | 69 | ABU, GOL |
| 5 | 363 | 0.75 | 0.85 | 53 | empty |
Interfaces
5 interfaces between chains.
- B–D · 674 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 621 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 389 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 128 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6EB3 · Structural and enzymatic characterization of an esterase from a metagenomic library · 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 6EB3 · PDBe 6EB3
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