Research workbench
Structure of N289A mutant of ampc in complex with SM2, carboxyphenylglycylboronic acid bearing the cephalothin R1 side chain
Analyse Structure of N289A mutant of ampc in complex with SM2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PI5
- Type
- protein
- Length
- 716 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
- SM2, K, PO4
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 39% helix, 23% strand | P00811 |
Ligands and binding sites
- SM2 · (1R)-1-(2-thienylacetylamino)-1-(3-carboxyphenyl) methylboronic acid · ligand · 3 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.79 | 0.84 | 71 | empty |
| 2 | 340 | 0.66 | 0.81 | 54 | SM2 |
| 3 | 316 | 0.58 | 0.77 | 48 | SM2 |
| 4 | 97 | 0.47 | 0.80 | 25 | empty |
| 5 | 63 | 0.31 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 631 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1PI5 · Structure of N289A mutant of AmpC in complex with SM2, carboxyphenylglycylboronic acid… · 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
- 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 1PI5 · PDBe 1PI5 · UniProt P00811
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