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Crystal structure of acetyl xylan esterase from bacillus pumilus, monoclinic crystal form I
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
- 3FVR
- Type
- protein
- Length
- 3,816 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 0.79
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Acetyl xylan esterase (EC 3.1.1.6) | protein | 320 | 38% helix, 22% strand | Q9K5F2 |
| B, D, E, M | Acetyl xylan esterase (EC 3.1.1.6) | protein | 318 | 38% helix, 21% strand | Q9K5F2 |
| F, G, H, L, N | Acetyl xylan esterase (EC 3.1.1.6) | protein | 317 | 38% helix, 21% strand | Q9K5F2 |
| I | Acetyl xylan esterase (EC 3.1.1.6) | protein | 319 | 38% 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 · 5 copies · chains C, E, D, B, F, I, N, G, L
- PG4 · Tetraethylene glycol · additive · 3 copies · chains C, D, E, G, L, H
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains H, I, N, G, M
- PGE · Triethylene glycol · additive · 2 copies · chains C, F
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 | 983 | 0.79 | 0.80 | 89 | empty |
| 2 | 1067 | 0.77 | 0.79 | 85 | PEG, PG4 |
| 3 | 1106 | 0.76 | 0.78 | 100 | GOL, PGE, PG4 |
| 4 | 1091 | 0.76 | 0.78 | 95 | GOL, PEG |
| 5 | 1171 | 0.76 | 0.78 | 98 | PG4, GOL |
Interfaces
24 interfaces between chains.
- H–L · 1189 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1188 Ų buried · 33 hydrogen bonds · protein-protein
- A–F · 1184 Ų buried · 34 hydrogen bonds · protein-protein
- I–N · 1184 Ų buried · 32 hydrogen bonds · protein-protein
- C–E · 1177 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3FVR · 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 3FVR · PDBe 3FVR · UniProt Q9K5F2
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