MolNFT v1 · #124067 · protein
Vim-2 metallo beta lactamase in complex with 3-(mercaptomethyl)-[1,1'- biphenyl]-4-carboxylic acid
5K48 · Beta-lactamase vim-2: “Vim-2 metallo beta lactamase in complex with 3-(mercaptomethyl)-[1,1'- biphenyl]-4-carboxylic acid”. X-ray diffraction, 2 ligands (S5Z, ZN), 3 pockets (best druggability 0.74). MolNFT v1 #124067 on GenesisL1…
- PDB
- 5K48
- Type
- protein
- Length
- 463 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase vim-2
- UniProt
- Q9K2N0
- Ligands
- S5Z, ZN
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase vim-2 | protein | 231 | 27% helix, 30% strand | Q9K2N0 |
| B | Beta-lactamase vim-2 | protein | 232 | 27% helix, 28% strand | Q9K2N0 |
Ligands and binding sites
- S5Z · 4-phenyl-2-(sulfanylmethyl)benzoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- FMT · Formic acid · additive · 5 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 | 558 | 0.74 | 0.82 | 53 | S5Z, ZN |
| 2 | 68 | 0.38 | 0.79 | 22 | empty |
| 3 | 50 | 0.34 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 576 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5K48 · VIM-2 Metallo Beta Lactamase in complex with 3-(mercaptomethyl)-[1,1'-biphenyl]-4-carboxyl… · 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 5K48 · PDBe 5K48 · UniProt Q9K2N0
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