Research workbench
X-ray crystal structure of oxa-24/40 K84D in complex with meropenem
Analyse X-ray crystal structure of oxa-24/40 K84D in complex with meropenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RPA
- Type
- protein
- Length
- 245 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q8RLA6
- Ligands
- MER, BCT, SO4
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 245 | 40% helix, 21% strand | Q8RLA6 |
Ligands and binding sites
- MER · (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid · ligand · chains A
- BCT · Bicarbonate ion · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.42 | 0.75 | 19 | MER |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7RPA · X-ray crystal structure of OXA-24/40 K84D in complex with meropenem · 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 Q8RLA6
- Elsewhere: RCSB PDB 7RPA · PDBe 7RPA · UniProt Q8RLA6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.