MolNFT v1 · #54931 · protein
Mannosylglycerate synthase in complex with lactate
2Y4J: “Mannosylglycerate synthase in complex with lactate”. X-ray diffraction, 2 ligands (LAC, NA), 5 pockets (best druggability 0.70). MolNFT v1 #54931 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Y4J
- Type
- protein
- Length
- 754 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
- LAC, NA
- Pockets
- 5 · best druggability 0.70
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 | 377 | 54% helix, 10% strand | Q9RFR0 |
| B | Mannosylglycerate synthase (EC 2.4.1.217) | protein | 377 | 54% helix, 10% strand | Q9RFR0 |
Ligands and binding sites
- LAC · Lactic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.70 | 0.79 | 52 | LAC |
| 2 | 545 | 0.67 | 0.78 | 51 | LAC, TRS |
| 3 | 139 | 0.58 | 0.83 | 27 | empty |
| 4 | 117 | 0.58 | 0.84 | 26 | empty |
| 5 | 195 | 0.55 | 0.79 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1159 Ų buried · 12 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 2Y4J · PDBe 2Y4J · UniProt Q9RFR0
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