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Crystal structure of 1,2-beta-oligoglucan phosphorylase from lachnoclostridium phytofermentans in complex with sophorose
Analyse Crystal structure of 1,2-beta-oligoglucan phosphorylase from lachnoclostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H40
- Type
- protein
- Length
- 2,226 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- EC
- 2.4.1.333
- UniProt
- A9KJS6
- Ligands
- BGC, CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein (EC 2.4.1.333) | protein | 1113 | 26% helix, 33% strand | A9KJS6 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.82 | 0.83 | 97 | GOL |
| 2 | 902 | 0.81 | 0.83 | 98 | GOL |
| 3 | 719 | 0.74 | 0.80 | 65 | BGC, GOL |
| 4 | 720 | 0.73 | 0.79 | 60 | BGC, GOL |
| 5 | 525 | 0.72 | 0.81 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 1111 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 5H40 · Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium… · 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 A9KJS6
- Elsewhere: RCSB PDB 5H40 · PDBe 5H40 · UniProt A9KJS6
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