Research workbench
Crystal structure of a GH1 beta-glucosidase retrieved from microbial metagenome of poraque amazon lake
Analyse Crystal structure of a GH1 beta-glucosidase retrieved from microbial metagenome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WKA
- Type
- protein
- Length
- 1,859 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase | protein | 467 | 44% helix, 16% strand | — |
| B | Beta-glucosidase | protein | 458 | 43% helix, 16% strand | — |
| C | Beta-glucosidase | protein | 466 | 43% helix, 16% strand | — |
| D | Beta-glucosidase | protein | 468 | 44% helix, 15% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.74 | 0.80 | 48 | GOL, PEG |
| 2 | 678 | 0.74 | 0.80 | 49 | GOL, PEG |
| 3 | 684 | 0.72 | 0.79 | 48 | GOL, PEG |
| 4 | 708 | 0.72 | 0.78 | 49 | GOL, PEG |
| 5 | 1143 | 0.72 | 0.75 | 104 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1438 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1323 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 434 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 332 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5WKA · Crystal structure of a GH1 beta-glucosidase retrieved from microbial metagenome of… · 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 5WKA · PDBe 5WKA
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