Research workbench
Dissection of mannosylglycerate synthase: an archetypal mannosyltransferase
Analyse Dissection of mannosylglycerate synthase: an archetypal mannosyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BO8
- Type
- protein
- Length
- 3,800 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannosylglycerate synthase
- EC
- 2.4.1.-
- UniProt
- Q9RFR0
- Ligands
- GDX, MN, CL
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Mannosylglycerate synthase (EC 2.4.1.-) | protein | 380 | 54% helix, 10% strand | Q9RFR0 |
Ligands and binding sites
- GDX · Guanosine 5'-(trihydrogen diphosphate), P'-D-mannopyranosyl ester · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- MN · Manganese (II) ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- CL · Chloride ion · ion · 10 copies · chains A, B, C, D, E, F, G, H, I, J
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 | 936 | 0.89 | 0.92 | 126 | GDX, MN, CL |
| 2 | 1193 | 0.89 | 0.90 | 133 | GDX, MN, CL |
| 3 | 933 | 0.88 | 0.90 | 99 | empty |
| 4 | 737 | 0.87 | 0.91 | 80 | empty |
| 5 | 606 | 0.80 | 0.86 | 58 | empty |
Interfaces
15 interfaces between chains.
- E–F · 1147 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1142 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1141 Ų buried · 14 hydrogen bonds · protein-protein
- I–J · 1137 Ų buried · 13 hydrogen bonds · protein-protein
- F–H · 1132 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2BO8 · Dissection of mannosylglycerate synthase: an archetypal mannosyltransferase · the same entry in another collection · chain J against J, TM-score 1.00
- Q9RFR0 · AlphaFold monomer V2.0 prediction for mannosylglycerate synthase (Q9RFR0) · a predicted model of the same protein · 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 Q9RFR0
- Elsewhere: RCSB PDB 2BO8 · PDBe 2BO8 · UniProt Q9RFR0
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