Research workbench
Exo-beta-D-glucosaminidase from pyrococcus furiosus
Analyse Exo-beta-D-glucosaminidase from pyrococcus furiosus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JOW
- Type
- protein
- Length
- 3,048 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- UniProt
- Q8U3U2
- Ligands
- CA
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-galactosidase | protein | 762 | 32% helix, 27% strand | Q8U3U2 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 copies · chains A, B, C, D
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 | 922 | 0.74 | 0.77 | 69 | MPD |
| 2 | 937 | 0.73 | 0.77 | 74 | MPD |
| 3 | 892 | 0.73 | 0.77 | 63 | MPD |
| 4 | 921 | 0.73 | 0.77 | 68 | MPD |
| 5 | 74 | 0.63 | 0.91 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3057 Ų buried · 73 hydrogen bonds · protein-protein
- C–D · 3038 Ų buried · 75 hydrogen bonds · protein-protein
- B–C · 458 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 446 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6JOW · Exo-beta-D-glucosaminidase from Pyrococcus furiosus · the same entry in another collection · chain D against D, 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 Q8U3U2
- Elsewhere: RCSB PDB 6JOW · PDBe 6JOW · UniProt Q8U3U2
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