Research workbench
Mannosylglycerate synthase in complex with mg-GDP
Analyse Mannosylglycerate synthase in complex with mg-GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y4K
- Type
- protein
- Length
- 758 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, MG, CL
- Pockets
- 7 · best druggability 0.78
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 | 53% helix, 10% strand | Q9RFR0 |
| B | Mannosylglycerate synthase (EC 2.4.1.217) | protein | 378 | 54% helix, 10% strand | Q9RFR0 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- FMT · Formic acid · additive · 6 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.78 | 0.82 | 69 | MG, GDP, CL, FMT |
| 2 | 536 | 0.74 | 0.82 | 50 | MG, GDP, CL, FMT |
| 3 | 246 | 0.65 | 0.83 | 39 | FMT |
| 4 | 130 | 0.58 | 0.84 | 27 | empty |
| 5 | 114 | 0.58 | 0.85 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 861 Ų buried · 5 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 2Y4K · PDBe 2Y4K · UniProt Q9RFR0
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