MolNFT v1 · #140517 · protein
Crystal structure of vim-2 metallo-beta-lactamase
5YD7 · Beta-lactamase class B vim-2: “Crystal structure of vim-2 metallo-beta-lactamase”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.63). MolNFT v1 #140517 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YD7
- 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
- EC
- 3.5.2.6
- UniProt
- Q9K2N0
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.63
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 (EC 3.5.2.6) | protein | 231 | 27% helix, 29% strand | Q9K2N0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.63 | 0.75 | 60 | ZN |
| 2 | 162 | 0.55 | 0.81 | 26 | ZN, FMT |
Interfaces
1 interface between chains.
- A–B · 98 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5YD7 · Crystal Structure OF 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 Q9K2N0
- Elsewhere: RCSB PDB 5YD7 · PDBe 5YD7 · UniProt Q9K2N0
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