MolNFT v1 · #163125 · protein
Crystal structure of the udp-bound glycosyltransferase domain from the ygt toxin
6RTG · Rtx toxin and CA2+-binding protein: “Crystal structure of the udp-bound glycosyltransferase domain from the ygt toxin”. X-ray diffraction, 3 ligands (UDP, MN, K), 3 pockets (best druggability 0.80). MolNFT v1 #163125 on GenesisL1…
- PDB
- 6RTG
- Type
- protein
- Length
- 503 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rtx toxin and CA2+-binding protein
- UniProt
- C4SH25
- Ligands
- UDP, MN, K
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rtx toxin and CA2+-binding protein | protein | 503 | 57% helix, 8% strand | C4SH25 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- K · Potassium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.80 | 0.82 | 103 | UDP, MN, K, EDO |
| 2 | 52 | 0.45 | 0.84 | 26 | empty |
| 3 | 96 | 0.37 | 0.75 | 15 | empty |
Compared structures
- 6RTG · Crystal structure of the UDP-bound glycosyltransferase domain from the YGT toxin · 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 C4SH25
- Elsewhere: RCSB PDB 6RTG · PDBe 6RTG · UniProt C4SH25
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