MolNFT v1 · #125878 · protein
Vim-2 metallo-beta-lactamase in complex with 2-(3-fluoro-4- hydroxyphenyl)-3-oxoisoindoline-4-carboxylic acid (compound 35)
5LM6 · Metallo-beta-lactamase vim-2: “Vim-2 metallo-beta-lactamase in complex with 2-(3-fluoro-4- hydroxyphenyl)-3-oxoisoindoline-4-carboxylic acid…”. X-ray diffraction, 2 ligands (H32, ZN), 2 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 5LM6
- Type
- protein
- Length
- 462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase vim-2
- UniProt
- Q9K2N0
- Ligands
- H32, ZN
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Metallo-beta-lactamase vim-2 | protein | 231 | 27% helix, 29% strand | Q9K2N0 |
Ligands and binding sites
- H32 · 2-(3-fluoranyl-4-oxidanyl-phenyl)-3-oxidanylidene-1~{H}-isoindole-4-carboxylic acid · ligand · chains A
- ZN · Zinc ion · metal · 6 copies · chains B, A
- FMT · Formic acid · additive · 4 copies · chains B, A
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 | 561 | 0.71 | 0.80 | 59 | H32 |
| 2 | 151 | 0.49 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- B–A · 517 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5LM6 · VIM-2 metallo-beta-lactamase in complex with 2-(3-fluoro-4-hydroxyphenyl)-3-oxoisoindoline… · the same entry in another collection · chain B against B, 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 5LM6 · PDBe 5LM6 · UniProt Q9K2N0
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