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Crystal structure of lactococcus lactis subsp. cremoris GH31 alpha-1, 3-glucosidase, P21 space group
Analyse Crystal structure of lactococcus lactis subsp. cremoris GH31 alpha-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WJ9
- Type
- protein
- Length
- 4,373 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-xylosidase
- EC
- 3.2.1.-
- UniProt
- A2RM80
- Ligands
- XYL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-xylosidase (EC 3.2.1.-) | protein | 733 | 28% helix, 24% strand | A2RM80 |
| B, C, D, F, E | Alpha-xylosidase (EC 3.2.1.-) | protein | 728 | 28% helix, 25% strand | A2RM80 |
Ligands and binding sites
- XYL · Xylitol · ligand · 6 copies · chains A, B, C, D, F, E
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, D, F, E
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 | 875 | 0.78 | 0.81 | 99 | empty |
| 2 | 897 | 0.78 | 0.80 | 105 | empty |
| 3 | 645 | 0.77 | 0.83 | 53 | empty |
| 4 | 628 | 0.77 | 0.82 | 42 | empty |
| 5 | 563 | 0.76 | 0.83 | 74 | empty |
Interfaces
12 interfaces between chains.
- B–F · 1367 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1366 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 1358 Ų buried · 12 hydrogen bonds · protein-protein
- F–E · 924 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 912 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7WJ9 · Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase, P21… · 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 A2RM80
- Elsewhere: RCSB PDB 7WJ9 · PDBe 7WJ9 · UniProt A2RM80
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