MolNFT v1 · #157438 · protein
Ctx-M-14 class a beta-lactamase in complex with avibactam at pH 7.9
6MZ2: “Ctx-M-14 class a beta-lactamase in complex with avibactam at pH 7.9”. X-ray diffraction, 4 ligands (NXL, K, NA), 2 pockets (best druggability 0.73). MolNFT v1 #157438 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MZ2
- Type
- protein
- Length
- 521 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A2S1PK93
- Ligands
- NXL, K, NA, PO4
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 263 | 44% helix, 19% strand | A0A2S1PK93 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 258 | 43% helix, 20% strand | A0A2S1PK93 |
Ligands and binding sites
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 13 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.73 | 0.79 | 89 | NXL, NA, K |
| 2 | 374 | 0.60 | 0.77 | 44 | K, NXL |
Interfaces
1 interface between chains.
- A–B · 639 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, cyclization).
Compared structures
- 6MZ2 · CTX-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 · 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 A0A2S1PK93
- Elsewhere: RCSB PDB 6MZ2 · PDBe 6MZ2 · UniProt A0A2S1PK93
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.