MolNFT v1 · #172550 · protein
Crystal structure of vim-2 with hydrolyzed faropenem (ring-open form)
7A60 · Beta-lactamase vim-2: “Crystal structure of vim-2 with hydrolyzed faropenem (ring-open form)”. X-ray diffraction, 2 ligands (QZH, ZN), 2 pockets (best druggability 0.72). MolNFT v1 #172550 on GenesisL1: 3D structure, binding sites…
- PDB
- 7A60
- Type
- protein
- Length
- 462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase vim-2
- UniProt
- Q9K2N0
- Ligands
- QZH, ZN
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase vim-2 | protein | 231 | 27% helix, 29% strand | Q9K2N0 |
Ligands and binding sites
- QZH · (5~{Z})-2-[1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-5-(4-oxidanylbutylidene)-2~{H}-1,3-thiazole-4-carboxylic 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
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 | 523 | 0.72 | 0.81 | 59 | ZN, QZH |
| 2 | 52 | 0.37 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 590 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7A60 · Crystal structure of VIM-2 with hydrolyzed faropenem (ring-open form) · 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 7A60 · PDBe 7A60 · UniProt Q9K2N0
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