Research workbench
Crystal structure of alpha-xylosidase from escherichia COLI
Analyse Crystal structure of alpha-xylosidase from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WE5
- Type
- protein
- Length
- 4,557 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative family 31 glucosidase yici
- EC
- 3.2.1.-
- UniProt
- P31434
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative family 31 glucosidase yici (EC 3.2.1.-) | protein | 772 | 22% helix, 34% strand | P31434 |
| B | Putative family 31 glucosidase yici (EC 3.2.1.-) | protein | 760 | 21% helix, 33% strand | P31434 |
| C | Putative family 31 glucosidase yici (EC 3.2.1.-) | protein | 756 | 21% helix, 33% strand | P31434 |
| D | Putative family 31 glucosidase yici (EC 3.2.1.-) | protein | 757 | 22% helix, 33% strand | P31434 |
| E | Putative family 31 glucosidase yici (EC 3.2.1.-) | protein | 755 | 21% helix, 33% strand | P31434 |
| F | Putative family 31 glucosidase yici (EC 3.2.1.-) | protein | 757 | 22% helix, 34% strand | P31434 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 6 copies · chains A, B, C, D, 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 | 164 | 0.80 | 0.96 | 47 | empty |
| 2 | 159 | 0.80 | 0.96 | 45 | empty |
| 3 | 931 | 0.78 | 0.80 | 98 | MES |
| 4 | 402 | 0.75 | 0.85 | 52 | MES |
| 5 | 88 | 0.73 | 0.96 | 23 | empty |
Interfaces
11 interfaces between chains.
- C–F · 2062 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 2051 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 2013 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1045 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 1039 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 114 modified (engineered).
Compared structures
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 P31434
- Elsewhere: RCSB PDB 1WE5 · PDBe 1WE5 · UniProt P31434
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