Research workbench
Structure of the multidrug ABC transporter SAV1866 from S. aureus in complex with AMP-pnp
Analyse Structure of the multidrug ABC transporter SAV1866 from S. aureus in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ONJ
- Type
- protein
- Length
- 1,156 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug export ATP-BINDING/PERMEASE protein SAV1866
- EC
- 3.6.3.-
- UniProt
- Q99T13
- Ligands
- ANP, NA
- Pockets
- 14 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Multidrug export ATP-BINDING/PERMEASE protein SAV1866 (EC 3.6.3.-) | protein | 578 | 64% helix, 10% strand | Q99T13 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.89 | 0.91 | 142 | NA, ANP |
| 2 | 646 | 0.76 | 0.82 | 62 | empty |
| 3 | 80 | 0.68 | 0.94 | 25 | empty |
| 4 | 81 | 0.65 | 0.92 | 26 | empty |
| 5 | 101 | 0.59 | 0.86 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 7172 Ų buried · 60 hydrogen bonds · protein-protein
Compared structures
- 2ONJ · Structure of the multidrug ABC transporter Sav1866 from S. aureus in complex with AMP-PNP · the same entry in another collection · chain A against A, TM-score 1.00
- Q99T13 · AlphaFold monomer V2.0 prediction for putative multidrug export ATP- BINDING/PERMEASE… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q99T13
- Elsewhere: RCSB PDB 2ONJ · PDBe 2ONJ · UniProt Q99T13
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