MolNFT v1 · #103936 · protein
Crystal structure of vim-2 metallo-beta-lactamase in complex with ML302 and ML302F
4PVO · Beta-lactamase class B vim-2: “Crystal structure of vim-2 metallo-beta-lactamase in complex with ML302 and ML302F”. X-ray diffraction, 3 ligands (S3C, SVB, ZN), 2 pockets (best druggability 0.72). MolNFT v1 #103936 on GenesisL1: 3D…
- PDB
- 4PVO
- Type
- protein
- Length
- 464 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
- S3C, SVB, ZN
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase class B vim-2 | protein | 231 | 27% helix, 29% strand | Q9K2N0 |
| B | Beta-lactamase class B vim-2 | protein | 233 | 27% helix, 29% strand | Q9K2N0 |
Ligands and binding sites
- S3C · (2Z)-2-sulfanyl-3-(2,3,6-trichlorophenyl)prop-2-enoic acid · ligand · 2 copies · chains A, B
- SVB · N-(4-methylpiperazin-1-yl)-2-[(5Z)-4-oxo-2-thioxo-5-(2,3,6-trichlorobenzylidene)-1,3-thiazolidin-3-yl]acetamide · ligand · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains 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 | 653 | 0.72 | 0.79 | 56 | ZN, S3C, SVB |
| 2 | 76 | 0.44 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 594 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4PVO · Crystal Structure of VIM-2 metallo-beta-lactamase in complex with ML302 and ML302F · 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 4PVO · PDBe 4PVO · UniProt Q9K2N0
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