Research workbench
1.1 resolution structure of ybff, a new esterase from escherichia COLI: a unique substrate-binding crevice generated by domain arrangement
Analyse 1.1 resolution structure of ybff, a new esterase from escherichia COLI: a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BF8
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Esterase ybff
- EC
- 3.1.-.-
- UniProt
- J7QD06
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Esterase ybff (EC 3.1.-.-) | protein | 255 | 40% helix, 15% strand | J7QD06 |
| B | Esterase ybff (EC 3.1.-.-) | protein | 254 | 42% helix, 15% strand | J7QD06 |
Ligands and binding sites
- MLA · Malonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.77 | 0.80 | 65 | empty |
| 2 | 61 | 0.69 | 0.96 | 22 | MLA |
| 3 | 60 | 0.68 | 0.95 | 22 | MLA |
| 4 | 105 | 0.37 | 0.74 | 21 | empty |
| 5 | 80 | 0.37 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 726 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3BF8 · 1.1 resolution structure of ybfF, a new esterase from Escherichia coli: a unique… · 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 J7QD06
- Elsewhere: RCSB PDB 3BF8 · PDBe 3BF8 · UniProt J7QD06
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