Research workbench
Crystal structure of acetyl xylan esterase from bacillus pumilus obtained in presence of D-xylose and sodium acetate
Analyse Crystal structure of acetyl xylan esterase from bacillus pumilus obtained in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FYU
- Type
- protein
- Length
- 3,800 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl xylan esterase
- EC
- 3.1.1.6
- UniProt
- Q9K5F2
- Ligands
- XYP, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acetyl xylan esterase (EC 3.1.1.6) | protein | 318 | 38% helix, 21% strand | Q9K5F2 |
| C, F, G, N | Acetyl xylan esterase (EC 3.1.1.6) | protein | 316 | 39% helix, 21% strand | Q9K5F2 |
| D | Acetyl xylan esterase (EC 3.1.1.6) | protein | 317 | 38% helix, 21% strand | Q9K5F2 |
| E, L, M | Acetyl xylan esterase (EC 3.1.1.6) | protein | 317 | 38% helix, 21% strand | Q9K5F2 |
| H, I | Acetyl xylan esterase (EC 3.1.1.6) | protein | 316 | 37% helix, 21% strand | Q9K5F2 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 7 copies · chains A, C, E, F, I, L, G, M, H, N
- CL · Chloride ion · ion · 18 copies · chains A, B, C, D, E, F, G, H, I, L, M, N
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, E, F, B, C, D, G, I, L, H, N, M
- ACY · Acetic acid · additive · 5 copies · chains C, E, F, G, I, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.79 | 0.81 | 95 | ACY, EDO |
| 2 | 985 | 0.78 | 0.80 | 75 | EDO, ACY |
| 3 | 1074 | 0.77 | 0.79 | 83 | empty |
| 4 | 866 | 0.77 | 0.80 | 71 | EDO, ACY |
| 5 | 1082 | 0.77 | 0.79 | 86 | ACY, EDO |
Interfaces
25 interfaces between chains.
- H–N · 1189 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 1189 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1183 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1182 Ų buried · 35 hydrogen bonds · protein-protein
- I–L · 1180 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (nonstandard).
Compared structures
- 3FYU · Crystal structure of acetyl xylan esterase from Bacillus pumilus obtained in presence of… · 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 3FYU · PDBe 3FYU · UniProt Q9K5F2
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