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Crystal structure of bacillus pumilus acetyl xylan esterase S181A mutant in complex with beta-D-xylopyranose
Analyse Crystal structure of bacillus pumilus acetyl xylan esterase S181A mutant in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FYT
- Type
- protein
- Length
- 3,761 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 · 7 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Acetyl xylan esterase (EC 3.1.1.6) | protein | 315 | 38% helix, 21% strand | Q9K5F2 |
| B, E | Acetyl xylan esterase (EC 3.1.1.6) | protein | 314 | 38% helix, 21% strand | Q9K5F2 |
| C, G | Acetyl xylan esterase (EC 3.1.1.6) | protein | 312 | 38% helix, 21% strand | Q9K5F2 |
| D | Acetyl xylan esterase (EC 3.1.1.6) | protein | 315 | 37% helix, 21% strand | Q9K5F2 |
| F, M | Acetyl xylan esterase (EC 3.1.1.6) | protein | 311 | 38% helix, 22% strand | Q9K5F2 |
| I, N | Acetyl xylan esterase (EC 3.1.1.6) | protein | 313 | 38% helix, 22% strand | Q9K5F2 |
| L | Acetyl xylan esterase (EC 3.1.1.6) | protein | 316 | 38% helix, 22% strand | Q9K5F2 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 6 copies · chains B, C, D, A, E, F, H, I, N, G, L, M
- CL · Chloride ion · ion · 34 copies · chains A, B, C, D, E, F, G, H, I, L, M, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.79 | 0.81 | 95 | empty |
| 2 | 941 | 0.78 | 0.80 | 87 | empty |
| 3 | 844 | 0.78 | 0.81 | 78 | XYP |
| 4 | 1133 | 0.77 | 0.79 | 94 | XYP |
| 5 | 1113 | 0.75 | 0.78 | 97 | XYP |
Interfaces
24 interfaces between chains.
- I–N · 1218 Ų buried · 33 hydrogen bonds · protein-protein
- H–L · 1199 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1193 Ų buried · 33 hydrogen bonds · protein-protein
- G–M · 1193 Ų buried · 33 hydrogen bonds · protein-protein
- A–F · 1178 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3FYT · Crystal structure of Bacillus pumilus acetyl xylan esterase S181A mutant in complex with… · the same entry in another collection · chain L against L, 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 3FYT · PDBe 3FYT · UniProt Q9K5F2
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