Research workbench
Crystal structure of an acetyl xylan esterase from a desert metagenome
Analyse Crystal structure of an acetyl xylan esterase from a desert metagenome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FKX
- Type
- protein
- Length
- 1,930 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl xylan esterase
- EC
- 3.1.1.72
- Ligands
- NA, SO4
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl xylan esterase (EC 3.1.1.72) | protein | 323 | 34% helix, 20% strand | — |
| B, D, E, F | Acetyl xylan esterase (EC 3.1.1.72) | protein | 322 | 35% helix, 20% strand | — |
| C | Acetyl xylan esterase (EC 3.1.1.72) | protein | 319 | 36% helix, 20% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, D, C, E, F
- SO4 · Sulfate ion · ion · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 13 copies · chains A, B, D, C, E, F
- FMT · Formic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.79 | 0.81 | 91 | empty |
| 2 | 847 | 0.78 | 0.81 | 80 | empty |
| 3 | 789 | 0.77 | 0.81 | 73 | empty |
| 4 | 1102 | 0.76 | 0.78 | 90 | empty |
| 5 | 724 | 0.76 | 0.81 | 63 | empty |
Interfaces
12 interfaces between chains.
- C–E · 849 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 849 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 842 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 821 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 817 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6FKX · Crystal structure of an acetyl xylan esterase from a desert metagenome · 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
- Elsewhere: RCSB PDB 6FKX · PDBe 6FKX
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