MolNFT v1 · #15233 · protein
Ampc beta-lactamase in complex with an M.CARBOXYPHENYLGLYCYLBORONIC acid bearing the cephalothin R1 side chain
1MY8: “Ampc beta-lactamase in complex with an M.CARBOXYPHENYLGLYCYLBORONIC acid bearing the cephalothin R1 side chain”. X-ray diffraction, 2 ligands (SM3, PO4), 7 pockets (best druggability 0.80). MolNFT v1 #15233 on GenesisL1: 3D…
- PDB
- 1MY8
- 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
- SM3, PO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 41% helix, 23% strand | P00811 |
Ligands and binding sites
- SM3 · (1R)-1-(2-thienylacetylamino)-1-phenylmethylboronic acid · ligand · 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.80 | 0.86 | 73 | empty |
| 2 | 392 | 0.68 | 0.81 | 57 | SM3 |
| 3 | 321 | 0.67 | 0.82 | 48 | SM3 |
| 4 | 76 | 0.47 | 0.82 | 22 | empty |
| 5 | 71 | 0.33 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 768 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1MY8 · AmpC beta-lactamase in complex with an M.carboxyphenylglycylboronic acid bearing the… · 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 1MY8 · PDBe 1MY8 · UniProt P00811
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