MolNFT v2 · #117125 · protein
1,2,4-Triazole-3-thione compounds as inhibitors of L1, di-zinc metallo-beta-lactamases.
5DPX · Metallo-beta-lactamase L1 type 3: “1,2,4-Triazole-3-thione compounds as inhibitors of L1, di-zinc metallo-beta-lactamases.”. X-ray diffraction at 1.85, 3 ligands (L3B, ZN, SO4), 6 pockets (best druggability 0.66). MolNFT v2 #117125…
- PDB
- 5DPX
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Stenotrophomonas maltophilia
- Molecule
- Metallo-beta-lactamase L1 type 3
- EC
- 3.5.2.6
- UniProt
- P52700
- Ligands
- L3B, ZN, SO4
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · resolution 1.85 · 1 distinct chain · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallo-beta-lactamase L1 type 3 (EC 3.5.2.6) | protein | 266 | 30% helix, 24% strand | P52700 |
Ligands and binding sites
- L3B · 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.66 | 0.82 | 34 | empty |
| 2 | 181 | 0.54 | 0.79 | 32 | L3B |
| 3 | 179 | 0.51 | 0.78 | 31 | L3B |
| 4 | 62 | 0.29 | 0.74 | 13 | empty |
| 5 | 57 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1303 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5DPX · 1,2,4-triazole-3-thione compounds as inhibitors of L1, di-zinc metallo-beta-lactamases. · the same entry in another collection · chain A against A, TM-score 1.00
- P52700 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase L1 type 3 (P52700) · a predicted model of the same protein · chain B 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 P52700
- Elsewhere: RCSB PDB 5DPX · PDBe 5DPX · UniProt P52700
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