MolNFT v1 · #154466 · protein
Crystal structure of a class C beta lactamase in complex with AMP
6KBY · Beta-lactamase: “Crystal structure of a class C beta lactamase in complex with AMP”. X-ray diffraction, 1 ligand (AMP), 2 pockets (best druggability 0.62). MolNFT v1 #154466 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6KBY
- Type
- protein
- Length
- 362 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q9XB24
- Ligands
- AMP
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 362 | 39% helix, 23% strand | Q9XB24 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 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 | 333 | 0.62 | 0.78 | 42 | AMP |
| 2 | 89 | 0.33 | 0.73 | 24 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6KBY · Crystal structure of a class C beta lactamase in complex with AMP · 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 Q9XB24
- Elsewhere: RCSB PDB 6KBY · PDBe 6KBY · UniProt Q9XB24
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