MolNFT v1 · #156976 · protein
Carbapenemase vcc-1 bound to avibactam
6MKQ · Beta-lactamase: “Carbapenemase vcc-1 bound to avibactam”. X-ray diffraction, 1 ligand (NXL), 1 pocket (best druggability 0.31). MolNFT v1 #156976 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MKQ
- Type
- protein
- Length
- 262 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A0U3IB62
- Ligands
- NXL
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 262 | 42% helix, 17% strand | A0A0U3IB62 |
Ligands and binding sites
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.31 | 0.74 | 16 | NXL |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 6MKQ · Carbapenemase VCC-1 bound to avibactam · 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 A0A0U3IB62
- Elsewhere: RCSB PDB 6MKQ · PDBe 6MKQ · UniProt A0A0U3IB62
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