MolNFT v1 · #28695 · protein
X-ray crystallographic structure of ctx-M-9 beta-lactamase complexed with a boronic acid inhibitor (SM2)
1YM1 · Beta-lactamase ctx-M-9A: “X-ray crystallographic structure of ctx-M-9 beta-lactamase complexed with a boronic acid inhibitor (SM2)”. X-ray diffraction, 2 ligands (SM2, PO4), 2 pockets (best druggability 0.29). MolNFT v1 #28695 on…
- PDB
- 1YM1
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase ctx-M-9A
- EC
- 3.5.2.6
- UniProt
- Q9L5C8
- Ligands
- SM2, PO4
- Pockets
- 2 · best druggability 0.29
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase ctx-M-9A (EC 3.5.2.6) | protein | 263 | 44% helix, 19% strand | Q9L5C8 |
| B | Beta-lactamase ctx-M-9A (EC 3.5.2.6) | protein | 260 | 44% helix, 20% strand | Q9L5C8 |
Ligands and binding sites
- SM2 · (1R)-1-(2-thienylacetylamino)-1-(3-carboxyphenyl) methylboronic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.29 | 0.76 | 19 | PO4, SM2 |
| 2 | 58 | 0.29 | 0.75 | 17 | PO4, SM2 |
Interfaces
1 interface between chains.
- A–B · 157 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1YM1 · X-ray crystallographic structure of CTX-M-9 beta-lactamase complexed with a boronic acid… · 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 Q9L5C8
- Elsewhere: RCSB PDB 1YM1 · PDBe 1YM1 · UniProt Q9L5C8
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