Research workbench
Structure of the retaining glycosyltransferase MSHA:THE first step in mycothiol biosynthesis. organism: corynebacterium glutamicum : complex with udp and 1L-ins-1- P.
Analyse Structure of the retaining glycosyltransferase MSHA:THE first step in mycothiol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C4V
- Type
- protein
- Length
- 786 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Predicted glycosyltransferases
- EC
- 2.4.1.-
- UniProt
- Q8NTA6
- Ligands
- UDP, LIP, MG
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Predicted glycosyltransferases (EC 2.4.1.-) | protein | 393 | 48% helix, 17% strand | Q8NTA6 |
| B | Predicted glycosyltransferases (EC 2.4.1.-) | protein | 393 | 47% helix, 18% strand | Q8NTA6 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- LIP · L-myo-inositol-1-phosphate · ligand · chains B
- MG · Magnesium ion · metal · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.78 | 0.84 | 86 | UDP, LIP |
| 2 | 562 | 0.77 | 0.84 | 79 | UDP |
| 3 | 960 | 0.72 | 0.76 | 75 | empty |
| 4 | 147 | 0.46 | 0.77 | 22 | MG |
| 5 | 159 | 0.45 | 0.76 | 26 | MG |
Interfaces
1 interface between chains.
- A–B · 656 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3C4V · Structure of the retaining glycosyltransferase MshA:The first step in mycothiol… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NTA6 · AlphaFold monomer V2.0 prediction for D-inositol 3-phosphate glycosyltransferase (Q8NTA6) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q8NTA6
- Elsewhere: RCSB PDB 3C4V · PDBe 3C4V · UniProt Q8NTA6
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