MolNFT v1 · #188668 · protein
Clavulanic acid-ctx-M-15
7U48 · Beta-lactamase: “Clavulanic acid-ctx-M-15”. X-ray diffraction, 2 ligands (LBX, SO4), 6 pockets (best druggability 0.51). MolNFT v1 #188668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7U48
- Type
- protein
- Length
- 792 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- C7S9T0
- Ligands
- LBX, SO4
- Pockets
- 6 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-lactamase (EC 3.5.2.6) | protein | 264 | 42% helix, 19% strand | C7S9T0 |
Ligands and binding sites
- LBX · (E)-5-hydroxy-3-oxo-N-(3-oxopropylidene)-L-norvaline · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.51 | 0.74 | 30 | empty |
| 2 | 243 | 0.49 | 0.74 | 33 | empty |
| 3 | 80 | 0.47 | 0.82 | 21 | empty |
| 4 | 94 | 0.34 | 0.74 | 18 | LBX, SO4 |
| 5 | 82 | 0.33 | 0.75 | 20 | LBX, SO4 |
Interfaces
2 interfaces between chains.
- A–B · 938 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 297 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7U48 · Clavulanic acid-CTX-M-15 · the same entry in another collection · chain C against C, 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 C7S9T0
- Elsewhere: RCSB PDB 7U48 · PDBe 7U48 · UniProt C7S9T0
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