Research workbench
Acetyl xylan esterase from bacillus pumilus CECT5072 bound to paraoxon
Analyse Acetyl xylan esterase from bacillus pumilus CECT5072 bound to paraoxon in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XLC
- Type
- protein
- Length
- 1,868 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl xylan esterase
- EC
- 3.1.1.72
- UniProt
- Q9K5F2
- Ligands
- DEP
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Acetyl xylan esterase (EC 3.1.1.72) | protein | 311 | 38% helix, 22% strand | Q9K5F2 |
| E, F | Acetyl xylan esterase (EC 3.1.1.72) | protein | 312 | 38% helix, 21% strand | Q9K5F2 |
Ligands and binding sites
- DEP · Diethyl phosphonate · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.79 | 0.80 | 87 | DEP |
| 2 | 1185 | 0.77 | 0.79 | 99 | DEP |
| 3 | 1031 | 0.77 | 0.79 | 90 | DEP |
| 4 | 50 | 0.71 | 0.99 | 18 | empty |
| 5 | 280 | 0.54 | 0.76 | 47 | empty |
Interfaces
12 interfaces between chains.
- A–D · 1197 Ų buried · 35 hydrogen bonds · protein-protein
- C–F · 1183 Ų buried · 31 hydrogen bonds · protein-protein
- B–E · 1167 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 851 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 849 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified, 6 covalent (engineered, covalent ligand).
Compared structures
- 2XLC · Acetyl xylan esterase from Bacillus pumilus CECT5072 bound to paraoxon · 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 Q9K5F2
- Elsewhere: RCSB PDB 2XLC · PDBe 2XLC · UniProt Q9K5F2
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