Research workbench
Vim-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphenyl)- 2-((S)-3-mercapto-2-METHYLPROPANAMIDO)ACETIC acid (compound 12)
Analyse Vim-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphenyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y6E
- 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
- 8PO, ZN
- Pockets
- 3 · best druggability 0.64
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
- 8PO · (2R)-2-(4-hydroxyphenyl)-2-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]ethanoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.64 | 0.76 | 51 | 8PO |
| 2 | 140 | 0.49 | 0.79 | 20 | ZN, 8PO |
| 3 | 66 | 0.36 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 259 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5Y6E · VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphenyl)-2-((S)-3-mercapto-2-m… · 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 5Y6E · PDBe 5Y6E · UniProt Q9K2N0
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