Research workbench
Crystal structure of streptogramin a acetyltransferase vata from staphylococcus aureus in complex with streptogramin analog F1037 (47)
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
- 6X3C
- Type
- protein
- Length
- 1,231 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virginiamycin a acetyltransferase
- EC
- 2.3.1.-
- UniProt
- P26839
- Ligands
- SXA, O7S, MG, PO4, CL, SO4
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virginiamycin a acetyltransferase (EC 2.3.1.-) | protein | 207 | 24% helix, 20% strand | P26839 |
| B | Virginiamycin a acetyltransferase (EC 2.3.1.-) | protein | 204 | 22% helix, 21% strand | P26839 |
| C | Virginiamycin a acetyltransferase (EC 2.3.1.-) | protein | 205 | 21% helix, 20% strand | P26839 |
| D, F | Virginiamycin a acetyltransferase (EC 2.3.1.-) | protein | 206 | 21% helix, 20% strand | P26839 |
| E | Virginiamycin a acetyltransferase (EC 2.3.1.-) | protein | 203 | 23% helix, 21% strand | P26839 |
Ligands and binding sites
- SXA · Thioacetic acid S-{2-[3-(2-hydroxy-3,3-dimethyl-4-phosphonooxy-butyrylamino)-propionylamino]-ethyl} ester · ligand · 6 copies · chains A, F, B, C, D, E
- O7S · (3r,4r,5e,10e,12e,14s,16r,26ar)-16-fluoro-14-hydroxy-12-methyl-3-(propan-2-yl)-4-(prop-2-en-1-yl)-3,4,8,9, 14,15,16,17,24,25,26,26A-dodecahydro-1H,7H,22H-21,18-(azeno)pyrrolo[2,1-C][1,8,4, 19]dioxadiazacyclotetracosine-1,7,22-trione · ligand · 6 copies · chains A, E, B, D, C, F
- MG · Magnesium ion · metal · 2 copies · chains B, C, D, A, E, F
- PO4 · Phosphate ion · ion · 14 copies · chains A, B, D, C, E, F
- CL · Chloride ion · ion · 6 copies · chains A, C, D, E, F
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.81 | 0.82 | 108 | O7S, CL, SXA |
| 2 | 585 | 0.77 | 0.83 | 60 | SXA, O7S |
| 3 | 593 | 0.76 | 0.82 | 58 | SXA, O7S |
| 4 | 908 | 0.76 | 0.79 | 79 | PO4, CL |
| 5 | 550 | 0.75 | 0.82 | 63 | SXA, O7S, CL |
Interfaces
9 interfaces between chains.
- B–C · 1424 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1417 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 1404 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 1403 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1393 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6X3C · 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 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 6X3C · PDBe 6X3C · UniProt P26839
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