MolNFT v1 · #141910 · protein
Crystal structure of GH31 alpha-xylosidase from a soil metagenome
5ZN6 · Alpha-xylosidase MEXYL31: “Crystal structure of GH31 alpha-xylosidase from a soil metagenome”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #141910 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZN6
- Type
- protein
- Length
- 5,421 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-xylosidase MEXYL31
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Alpha-xylosidase MEXYL31 | protein | 680 | 25% helix, 31% strand | — |
| B | Alpha-xylosidase MEXYL31 | protein | 682 | 25% helix, 30% strand | — |
| C, H | Alpha-xylosidase MEXYL31 | protein | 676 | 25% helix, 30% strand | — |
| E, F | Alpha-xylosidase MEXYL31 | protein | 675 | 25% helix, 31% strand | — |
| G | Alpha-xylosidase MEXYL31 | protein | 677 | 25% helix, 31% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 52 copies · chains A, C, B, G, D, H, E, 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 | 672 | 0.86 | 0.90 | 97 | empty |
| 2 | 396 | 0.81 | 0.89 | 58 | empty |
| 3 | 369 | 0.80 | 0.89 | 53 | empty |
| 4 | 254 | 0.78 | 0.91 | 37 | GOL |
| 5 | 271 | 0.78 | 0.90 | 37 | GOL |
Interfaces
12 interfaces between chains.
- A–C · 1521 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1504 Ų buried · 22 hydrogen bonds · protein-protein
- D–H · 1496 Ų buried · 22 hydrogen bonds · protein-protein
- B–G · 1489 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 1414 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5ZN6 · Crystal structure of GH31 alpha-xylosidase from a soil metagenome · the same entry in another collection · chain H against H, 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 5ZN6 · PDBe 5ZN6
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