Research workbench
X-ray crystal structure of ampc S64G mutant beta-lactamase
Analyse X-ray crystal structure of ampc S64G mutant beta-lactamase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L0G
- Type
- protein
- Length
- 713 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P00811
- Ligands
- GLC, FRU, PO4
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 355 | 39% helix, 24% strand | P00811 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 41% helix, 23% strand | P00811 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A
- FRU · beta-D-fructofuranose · sugar · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.80 | 0.90 | 43 | empty |
| 2 | 598 | 0.71 | 0.79 | 53 | GLC, FRU, PO4 |
| 3 | 334 | 0.68 | 0.82 | 54 | PO4 |
| 4 | 117 | 0.55 | 0.83 | 16 | empty |
| 5 | 73 | 0.50 | 0.84 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 774 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1L0G · X-ray Crystal Structure of AmpC S64G Mutant beta-Lactamase · the same entry in another collection · chain B against B, TM-score 1.00
- 1L2S · X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with a… · a predicted model of the same protein · chain B against B, TM-score 1.00
- P00811 · AlphaFold monomer V2.0 prediction for beta-lactamase (P00811) · a predicted model of the same protein · chain B 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 P00811
- Elsewhere: RCSB PDB 1L0G · PDBe 1L0G · UniProt P00811
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