MolNFT v1 · #148288 · protein
Methylglyoxal synthase mgsa from bacillus subtilis
6F2C: “Methylglyoxal synthase mgsa from bacillus subtilis”. X-ray diffraction, 1 ligand (CL), 13 pockets (best druggability 0.89). MolNFT v1 #148288 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6F2C
- Type
- protein
- Length
- 1,468 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylglyoxal synthase
- EC
- 4.2.3.3
- UniProt
- P42980
- Ligands
- CL
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylglyoxal synthase (EC 4.2.3.3) | protein | 124 | 52% helix, 18% strand | P42980 |
| D, B, F, C, E, H, K, L, J | Methylglyoxal synthase (EC 4.2.3.3) | protein | 122 | 52% helix, 18% strand | P42980 |
| G | Methylglyoxal synthase (EC 4.2.3.3) | protein | 123 | 54% helix, 18% strand | P42980 |
| I | Methylglyoxal synthase (EC 4.2.3.3) | protein | 123 | 50% helix, 18% strand | P42980 |
Ligands and binding sites
- CL · Chloride ion · ion · 19 copies · chains A, D, F, C, E, H, K, G, I, L
- GOL · Glycerol · additive · 9 copies · chains A, G, B, C, D, E, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.89 | 0.93 | 93 | CL |
| 2 | 815 | 0.88 | 0.91 | 92 | empty |
| 3 | 593 | 0.70 | 0.79 | 78 | GOL, CL |
| 4 | 73 | 0.39 | 0.79 | 20 | GOL |
| 5 | 73 | 0.38 | 0.79 | 21 | CL |
Interfaces
27 interfaces between chains.
- I–J · 906 Ų buried · 20 hydrogen bonds · protein-protein
- K–L · 903 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 901 Ų buried · 21 hydrogen bonds · protein-protein
- H–G · 899 Ų buried · 19 hydrogen bonds · protein-protein
- F–E · 897 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6F2C · Methylglyoxal synthase MgsA from Bacillus subtilis · the same entry in another collection · chain J against J, 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 P42980
- Elsewhere: RCSB PDB 6F2C · PDBe 6F2C · UniProt P42980
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