MolNFT v1 · #119251 · protein
Crystal structure of the metallo-beta-lactamase vim-2 with 2C
5FQC: “Crystal structure of the metallo-beta-lactamase vim-2 with 2C”. X-ray diffraction, 2 ligands (OK3, ZN), 2 pockets (best druggability 0.73). MolNFT v1 #119251 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FQC
- Type
- protein
- Length
- 462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q9K2N0
- Ligands
- OK3, ZN
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 231 | 27% helix, 29% strand | Q9K2N0 |
Ligands and binding sites
- OK3 · (4~{R})-4-[[4-(aminomethyl)phenyl]carbonylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-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
- 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 | 539 | 0.73 | 0.81 | 62 | ZN, OK3 |
| 2 | 53 | 0.39 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 574 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5FQC · Crystal structure of the metallo-beta-lactamase VIM-2 with 2C · 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 5FQC · PDBe 5FQC · UniProt Q9K2N0
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