Research workbench
Oxa-48 bound by compound 4.3
Analyse Oxa-48 bound by compound 4.3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L8O
- Type
- protein
- Length
- 968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- XV7, NA, CL
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 41% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- XV7 · 9H-fluorene-2,7-disulfonate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.69 | 0.80 | 44 | EDO |
| 2 | 468 | 0.68 | 0.79 | 41 | EDO |
| 3 | 352 | 0.61 | 0.78 | 45 | empty |
| 4 | 412 | 0.61 | 0.76 | 56 | XV7 |
| 5 | 324 | 0.60 | 0.78 | 45 | empty |
Interfaces
5 interfaces between chains.
- B–D · 456 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 444 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 295 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 287 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 180 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 7L8O · OXA-48 bound by Compound 4.3 · 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 Q6XEC0
- Elsewhere: RCSB PDB 7L8O · PDBe 7L8O · UniProt Q6XEC0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.