Research workbench
Oxa-23 meropenem complex
Analyse Oxa-23 meropenem complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JF4
- Type
- protein
- Length
- 483 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q9L4P2
- Ligands
- MER
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 21% strand | Q9L4P2 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 241 | 39% helix, 22% strand | Q9L4P2 |
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 · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.50 | 0.76 | 32 | MER |
| 2 | 200 | 0.50 | 0.76 | 36 | MER |
| 3 | 125 | 0.38 | 0.74 | 21 | empty |
| 4 | 83 | 0.37 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 476 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4JF4 · OXA-23 meropenem complex · 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 Q9L4P2
- Elsewhere: RCSB PDB 4JF4 · PDBe 4JF4 · UniProt Q9L4P2
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