Research workbench
Crystal structure of 1,2-beta-oligoglucan phosphorylase from lachnoclostridium phytofermentans in complex with alpha-D-glucose-1- phosphate
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
- 5H42
- Type
- protein
- Length
- 2,221 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
- G1P, GLC
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein (EC 2.4.1.333) | protein | 1108 | 26% helix, 33% strand | A9KJS6 |
| B | Uncharacterized protein (EC 2.4.1.333) | protein | 1113 | 26% helix, 33% strand | A9KJS6 |
Ligands and binding sites
- G1P · 1-O-phosphono-alpha-D-glucopyranose · ligand · 3 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.77 | 0.82 | 74 | empty |
| 2 | 699 | 0.75 | 0.80 | 64 | G1P |
| 3 | 745 | 0.75 | 0.80 | 67 | G1P |
| 4 | 370 | 0.74 | 0.85 | 48 | empty |
| 5 | 389 | 0.74 | 0.84 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 1092 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5H42 · 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 5H42 · PDBe 5H42 · UniProt A9KJS6
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