MolNFT v2 · #216663 · protein
Crystal structure of the metallo-beta-lactamase VIM1 with 3193
8PGP · Beta-lactamase VIM-1: “Crystal structure of the metallo-beta-lactamase VIM1 with 3193”. X-ray diffraction at 0.97, 2 ligands (YSR, ZN), 1 pocket (best druggability 0.53). MolNFT v2 #216663 on GenesisL1: 3D structure, binding sites…
- PDB
- 8PGP
- Type
- protein
- Length
- 232 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 0.97
- Source
- Pseudomonas aeruginosa
- Molecule
- Beta-lactamase VIM-1
- UniProt
- Q9XAY4
- Ligands
- YSR, ZN
- Pockets
- 1 · best druggability 0.53
Structure
x-ray diffraction · resolution 0.97 · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase VIM-1 | protein | 232 | 27% helix, 29% strand | Q9XAY4 |
Ligands and binding sites
- YSR · 7-[(1~{S})-1-[5-[(3-azanylazetidin-1-yl)methyl]-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-[3-cyano-4-(methylsulfonylamino)phenyl]-1~{H}-indole-2-carboxylic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.53 | 0.79 | 27 | YSR |
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 Q9XAY4
- Elsewhere: RCSB PDB 8PGP · PDBe 8PGP · UniProt Q9XAY4
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