Research workbench
Crystal structure of streptogramin a acetyltransferase vata from staphylococcus aureus in complex with streptogramin analog F0224 (46)
Analyse Crystal structure of streptogramin a acetyltransferase vata from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X3J
- Type
- protein
- Length
- 1,239 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virginiamycin a ACETYLTRANSFERASE,VATA
- EC
- 2.3.1.-
- UniProt
- P26839
- Ligands
- O7V, SXA, MG, CL, PO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Virginiamycin a ACETYLTRANSFERASE,VATA (EC 2.3.1.-) | protein | 206 | 23% helix, 20% strand | P26839 |
| C | Virginiamycin a ACETYLTRANSFERASE,VATA (EC 2.3.1.-) | protein | 209 | 25% helix, 20% strand | P26839 |
| D, E | Virginiamycin a ACETYLTRANSFERASE,VATA (EC 2.3.1.-) | protein | 207 | 26% helix, 20% strand | P26839 |
| F | Virginiamycin a ACETYLTRANSFERASE,VATA (EC 2.3.1.-) | protein | 204 | 22% helix, 21% strand | P26839 |
Ligands and binding sites
- O7V · (2R)-2-[(3s,4r,5e,10e,12e,14s,16r,26ar)-16-fluoro-14-hydroxy-4,12-dimethyl-1,7,22-trioxo-4,7,8,9,14,15,16, 17,24,25,26,26A-dodecahydro-1H,3H,22H-21,18-(azeno) pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-3-yl]propyl isoquinolin-3-ylcarbamate · ligand · 6 copies · chains A, D, B, C, E, F
- SXA · Thioacetic acid S-{2-[3-(2-hydroxy-3,3-dimethyl-4-phosphonooxy-butyrylamino)-propionylamino]-ethyl} ester · ligand · 6 copies · chains A, B, D, C, E, F
- MG · Magnesium ion · metal · 2 copies · chains C, E, F, A, B, D
- CL · Chloride ion · ion · 11 copies · chains B, C, F, E
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.77 | 0.84 | 61 | O7V, SXA |
| 2 | 550 | 0.76 | 0.83 | 59 | O7V, SXA |
| 3 | 551 | 0.76 | 0.83 | 59 | O7V, SXA |
| 4 | 513 | 0.75 | 0.83 | 60 | SXA, O7V |
| 5 | 487 | 0.75 | 0.83 | 61 | O7V, CL, SXA |
Interfaces
9 interfaces between chains.
- C–E · 1440 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 1427 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1411 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1405 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1389 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6X3J · Crystal structure of streptogramin A acetyltransferase VatA from Staphylococcus aureus in… · the same entry in another collection · chain F against F, TM-score 1.00
- P26839 · AlphaFold monomer V2.0 prediction for virginiamycin a acetyltransferase (P26839) · a predicted model of the same protein · chain A 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 6X3J · PDBe 6X3J · UniProt P26839
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