Research workbench
Crystal structure of acetyl xylan esterase from bacillus pumilus, monoclinic crystal form II
Analyse Crystal structure of acetyl xylan esterase from bacillus pumilus, monoclinic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FVT
- Type
- protein
- Length
- 3,808 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
- CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M, N | Acetyl xylan esterase (EC 3.1.1.6) | protein | 318 | 39% helix, 21% strand | Q9K5F2 |
| B, D, E, G, H, I, L | Acetyl xylan esterase (EC 3.1.1.6) | protein | 317 | 38% helix, 21% strand | Q9K5F2 |
| C | Acetyl xylan esterase (EC 3.1.1.6) | protein | 316 | 39% helix, 22% strand | Q9K5F2 |
| F | Acetyl xylan esterase (EC 3.1.1.6) | protein | 319 | 39% helix, 21% strand | Q9K5F2 |
Ligands and binding sites
- CL · Chloride ion · ion · 24 copies · chains A, B, C, D, E, F, G, H, I, L, M, N
- GOL · Glycerol · additive · 2 copies · chains E, G, M
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 | 887 | 0.78 | 0.81 | 83 | empty |
| 2 | 838 | 0.78 | 0.81 | 75 | empty |
| 3 | 862 | 0.77 | 0.80 | 76 | empty |
| 4 | 852 | 0.77 | 0.80 | 78 | GOL |
| 5 | 802 | 0.77 | 0.81 | 75 | empty |
Interfaces
25 interfaces between chains.
- B–D · 1208 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 1206 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1201 Ų buried · 32 hydrogen bonds · protein-protein
- H–N · 1197 Ų buried · 31 hydrogen bonds · protein-protein
- I–L · 1189 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3FVT · Crystal Structure of Acetyl Xylan Esterase from Bacillus pumilus, monoclinic crystal form… · 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 3FVT · PDBe 3FVT · UniProt Q9K5F2
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