Research workbench
Structure of streptogramin acetyltransferase in complex with an inhibitor
Analyse Structure of streptogramin acetyltransferase in complex with an inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DHO
- Type
- protein
- Length
- 1,218 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptogramin a acetyltransferase
- EC
- 2.3.1.-
- UniProt
- P50870
- Ligands
- B2M
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Streptogramin a acetyltransferase (EC 2.3.1.-) | protein | 203 | 27% helix, 22% strand | P50870 |
Ligands and binding sites
- B2M · 6-bromo-N'-[(1Z)-(3,5-dichloro-2-hydroxyphenyl)methylidene]-2-methylquinoline-4-carbohydrazide · ligand · 6 copies · chains A, C, B, D, F, E
- FMT · Formic acid · additive · 9 copies · chains A, B, C, D, E, F
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.79 | 0.80 | 86 | FMT, B2M |
| 2 | 1116 | 0.78 | 0.80 | 119 | DMS, B2M |
| 3 | 751 | 0.76 | 0.80 | 84 | B2M |
| 4 | 495 | 0.72 | 0.81 | 57 | B2M |
| 5 | 509 | 0.72 | 0.81 | 61 | B2M |
Interfaces
8 interfaces between chains.
- B–C · 1338 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1332 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1324 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1318 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1299 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3DHO · Structure of Streptogramin Acetyltransferase in Complex with an Inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
- P50870 · AlphaFold monomer V2.0 prediction for streptogramin a acetyltransferase (P50870) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P50870
- Elsewhere: RCSB PDB 3DHO · PDBe 3DHO · UniProt P50870
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