Research workbench
Metallo-beta-lactamase vim-2 in complex with dual MBL/SBL inhibitor MS19
Analyse Metallo-beta-lactamase vim-2 in complex with dual MBL/SBL inhibitor MS19 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JN6
- Type
- protein
- Length
- 462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase class B vim-2
- UniProt
- Q9K2N0
- Ligands
- BY0, ZN
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase class B vim-2 | protein | 231 | 27% helix, 29% strand | Q9K2N0 |
Ligands and binding sites
- BY0 · [(1S)-2-(1-benzofuran-3-yl)-1-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]ethyl]boronic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- FMT · Formic acid · additive · 6 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 | 502 | 0.68 | 0.79 | 60 | ZN, BY0, FMT |
| 2 | 59 | 0.37 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 542 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6JN6 · Metallo-Beta-Lactamase VIM-2 in complex with Dual MBL/SBL Inhibitor MS19 · 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 Q9K2N0
- Elsewhere: RCSB PDB 6JN6 · PDBe 6JN6 · UniProt Q9K2N0
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