Research workbench
Crystal structure of macrolide-efflux protein SP_1110 from streptococcus pneumoniae
Analyse Crystal structure of macrolide-efflux protein SP_1110 from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OP1
- Type
- protein
- Length
- 861 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrolide-efflux protein
- UniProt
- Q97QT9
- Ligands
- SO4, CL
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Macrolide-efflux protein | protein | 297 | 30% helix, 30% strand | Q97QT9 |
| B | Macrolide-efflux protein | protein | 304 | 32% helix, 31% strand | Q97QT9 |
| C | Macrolide-efflux protein | protein | 260 | 30% helix, 33% strand | Q97QT9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · 12 copies · chains A, C, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- ACY · Acetic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.73 | 0.83 | 58 | SO4, GOL |
| 2 | 638 | 0.73 | 0.80 | 74 | GOL, PEG, CL |
| 3 | 738 | 0.71 | 0.77 | 60 | empty |
| 4 | 358 | 0.68 | 0.81 | 39 | SO4, GOL, ACY |
| 5 | 441 | 0.66 | 0.79 | 46 | SO4, GOL, PEG |
Interfaces
3 interfaces between chains.
- A–B · 1442 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 370 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 3OP1 · Crystal Structure of Macrolide-efflux Protein SP_1110 from Streptococcus pneumoniae · the same entry in another collection · chain A against A, TM-score 1.00
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 Q97QT9
- Elsewhere: RCSB PDB 3OP1 · PDBe 3OP1 · UniProt Q97QT9
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