MolNFT v1 · #186230 · protein
Oxa-48 bound by compound 3.3
7R6Z · Beta-lactamase: “Oxa-48 bound by compound 3.3”. X-ray diffraction, 2 ligands (3I0, CL), 2 pockets (best druggability 0.77). MolNFT v1 #186230 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7R6Z
- Type
- protein
- Length
- 484 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- 3I0, CL
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 41% helix, 20% strand | Q6XEC0 |
Ligands and binding sites
- 3I0 · 4-amino-5-hydroxynaphthalene-2,7-disulfonic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.77 | 0.80 | 126 | 3I0, DMS, EDO, CL |
| 2 | 56 | 0.34 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1006 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 7R6Z · OXA-48 bound by Compound 3.3 · 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 7R6Z · PDBe 7R6Z · UniProt Q6XEC0
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