MolNFT v1 · #157763 · protein
Beta-lactamase from escherichia COLI str. sakai
6N9K: “Beta-lactamase from escherichia COLI str. sakai”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.68). MolNFT v1 #157763 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6N9K
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q8XDQ2
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 360 | 40% helix, 23% strand | Q8XDQ2 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 357 | 40% helix, 23% strand | Q8XDQ2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.68 | 0.82 | 56 | SO4 |
| 2 | 318 | 0.67 | 0.82 | 57 | SO4 |
| 3 | 613 | 0.62 | 0.74 | 65 | EDO |
| 4 | 88 | 0.34 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 182 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6N9K · Beta-lactamase from Escherichia coli str. Sakai · 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 Q8XDQ2
- Elsewhere: RCSB PDB 6N9K · PDBe 6N9K · UniProt Q8XDQ2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.