Research workbench
Mannosylglycerate synthase in complex with manganese and GDP
Analyse Mannosylglycerate synthase in complex with manganese and GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y4L
- Type
- protein
- Length
- 757 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannosylglycerate synthase
- EC
- 2.4.1.217
- UniProt
- Q9RFR0
- Ligands
- GDP, MN
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannosylglycerate synthase (EC 2.4.1.217) | protein | 380 | 54% helix, 10% strand | Q9RFR0 |
| B | Mannosylglycerate synthase (EC 2.4.1.217) | protein | 377 | 54% helix, 10% strand | Q9RFR0 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- MLI · Malonate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.79 | 0.85 | 58 | MN, GDP, MLI |
| 2 | 917 | 0.78 | 0.81 | 79 | MN, GDP, MLI |
| 3 | 299 | 0.64 | 0.80 | 39 | empty |
| 4 | 162 | 0.57 | 0.82 | 27 | empty |
| 5 | 158 | 0.57 | 0.82 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 827 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 2Y4L · PDBe 2Y4L · UniProt Q9RFR0
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