Research workbench
Crystallographic investigation of inhibition mode of the vim-2 metallo-beta-lactamase from pseudomonas aeruginosa with mercaptocarboxylate inhibitor
Analyse Crystallographic investigation of inhibition mode of the vim-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YZ3
- Type
- protein
- Length
- 450 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q7BJM5
- Ligands
- M5P, ZN, SO4
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallo-beta-lactamase (EC 3.5.2.6) | protein | 225 | 26% helix, 31% strand | Q7BJM5 |
Ligands and binding sites
- M5P · (S)-2-(mercaptomethyl)-5-phenylpentanoic acid · 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.58 | 0.80 | 24 | ZN, M5P |
| 2 | 201 | 0.55 | 0.79 | 30 | M5P |
| 3 | 94 | 0.42 | 0.78 | 28 | empty |
| 4 | 58 | 0.40 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 473 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2YZ3 · Crystallographic Investigation of Inhibition Mode of the VIM-2 Metallo-beta-lactamase… · 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 Q7BJM5
- Elsewhere: RCSB PDB 2YZ3 · PDBe 2YZ3 · UniProt Q7BJM5
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