Research workbench
Crystal structure of the E. COLI ampc beta-lactamase mutant N152A covalently acylated with the inhibitory beta-lactam, moxalactam
Analyse Crystal structure of the E. COLI ampc beta-lactamase mutant N152A covalently… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I5Q
- Type
- protein
- Length
- 714 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
- MOX
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 356 | 38% helix, 24% strand | P00811 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 41% helix, 23% strand | P00811 |
Ligands and binding sites
- MOX · (2R)-2-[(1R)-1-{[(2S)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}-1-methoxy-2-oxoethyl]-5-methylidene-5,6-dihydro-2H-1,3-oxazine-4-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.82 | 0.92 | 58 | empty |
| 2 | 563 | 0.73 | 0.81 | 60 | MOX |
| 3 | 396 | 0.69 | 0.82 | 52 | MOX |
| 4 | 89 | 0.45 | 0.80 | 22 | empty |
| 5 | 134 | 0.39 | 0.73 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 855 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1I5Q · Crystal structure of the E. COLI ampc beta-lactamase mutant N152A covalently acylated… · the same entry in another collection · 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
- 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
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 1I5Q · PDBe 1I5Q · UniProt P00811
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