MolNFT v1 · #94370 · protein
Crystal structure of streptogramin group a antibiotic acetyltransferase vata from staphylococcus aureus in complex with virginiamycin M1
4HUS · Virginiamycin a acetyltransferase: “Crystal structure of streptogramin group a antibiotic acetyltransferase vata from staphylococcus aureus in…”. X-ray diffraction, 4 ligands (VIR, NA, CL), 5 pockets (best druggability 0.76). MolNFT…
- PDB
- 4HUS
- Type
- protein
- Length
- 635 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virginiamycin a acetyltransferase
- EC
- 2.3.1.-
- UniProt
- P26839
- Ligands
- VIR, NA, CL, SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virginiamycin a acetyltransferase (EC 2.3.1.-) | protein | 212 | 27% helix, 20% strand | P26839 |
| B | Virginiamycin a acetyltransferase (EC 2.3.1.-) | protein | 214 | 27% helix, 20% strand | P26839 |
| C | Virginiamycin a acetyltransferase (EC 2.3.1.-) | protein | 209 | 27% helix, 20% strand | P26839 |
Ligands and binding sites
- VIR · Virginiamycin M1 · ligand · chains A, C
- NA · Sodium ion · metal · chains A, B, C
- CL · Chloride ion · ion · 9 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, C, B
- PGE · Triethylene glycol · additive · 2 copies · chains B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.76 | 0.81 | 62 | PEG, VIR |
| 2 | 692 | 0.75 | 0.80 | 70 | EDO, PEG, PGE |
| 3 | 629 | 0.74 | 0.81 | 64 | EDO, PGE |
| 4 | 604 | 0.71 | 0.79 | 52 | EDO, CL |
| 5 | 58 | 0.27 | 0.73 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1415 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1404 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1391 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4HUS · Crystal structure of streptogramin group A antibiotic acetyltransferase VatA from… · the same entry in another collection · chain A against A, TM-score 1.00
- P26839 · AlphaFold monomer V2.0 prediction for virginiamycin a acetyltransferase (P26839) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P26839
- Elsewhere: RCSB PDB 4HUS · PDBe 4HUS · UniProt P26839
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.