MolNFT v1 · #108434 · protein
Glycosyltransferase C from streptococcus agalactiae
4W6Q · Glucosyltransferase: “Glycosyltransferase C from streptococcus agalactiae”. X-ray diffraction, 2 ligands (UDP, SER), 15 pockets (best druggability 0.78). MolNFT v1 #108434 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4W6Q
- Type
- protein
- Length
- 1,327 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosyltransferase
- UniProt
- Q3D9X5
- Ligands
- UDP, SER
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosyltransferase | protein | 331 | 41% helix, 19% strand | Q3D9X5 |
| B, C, D | Glucosyltransferase | protein | 332 | 40% helix, 19% strand | Q3D9X5 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- SER · Serine · ligand · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.78 | 0.86 | 52 | empty |
| 2 | 377 | 0.77 | 0.87 | 62 | UDP |
| 3 | 434 | 0.77 | 0.86 | 48 | empty |
| 4 | 227 | 0.75 | 0.89 | 41 | UDP |
| 5 | 219 | 0.74 | 0.89 | 40 | UDP |
Interfaces
6 interfaces between chains.
- B–C · 1252 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1229 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1141 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1121 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 330 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4W6Q · Glycosyltransferase C from Streptococcus agalactiae · the same entry in another collection · chain A against A, 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 Q3D9X5
- Elsewhere: RCSB PDB 4W6Q · PDBe 4W6Q · UniProt Q3D9X5
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