MolNFT v1 · #116949 · protein
Fragments bound to the oxa-48 beta-lactamase: compound 17
5DTK: “Fragments bound to the oxa-48 beta-lactamase: compound 17”. X-ray diffraction, 2 ligands (5F3, CL), 8 pockets (best druggability 0.80). MolNFT v1 #116949 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DTK
- Type
- protein
- Length
- 972 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
- 5F3, CL
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 40% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- 5F3 · 3,5-di(pyridin-4-yl)benzoic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, D, C
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.80 | 0.82 | 125 | EDO, 5F3 |
| 2 | 684 | 0.77 | 0.82 | 93 | CL, EDO |
| 3 | 317 | 0.69 | 0.83 | 43 | EDO |
| 4 | 171 | 0.43 | 0.74 | 31 | 5F3 |
| 5 | 50 | 0.38 | 0.81 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–D · 983 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 458 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 449 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 267 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5DTK · Fragments bound to the OXA-48 beta-lactamase: Compound 17 · 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 5DTK · PDBe 5DTK · UniProt Q6XEC0
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