Research workbench
X-ray crystallographic structure of ctx-M-9 beta-lactamase complexed with nafcinin-like boronic acid inhibitor
Analyse X-ray crystallographic structure of ctx-M-9 beta-lactamase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YMS
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase ctx-M-9
- EC
- 3.5.2.6
- UniProt
- Q9L5C8
- Ligands
- NBF
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase ctx-M-9 (EC 3.5.2.6) | protein | 263 | 43% helix, 19% strand | Q9L5C8 |
| B | Beta-lactamase ctx-M-9 (EC 3.5.2.6) | protein | 261 | 43% helix, 19% strand | Q9L5C8 |
Ligands and binding sites
- NBF · [(2-ethoxy-1-naphthoyl)amino]methylboronic acid · ligand · 2 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 | 96 | 0.38 | 0.76 | 26 | NBF |
| 2 | 67 | 0.30 | 0.75 | 22 | NBF |
Interfaces
1 interface between chains.
- A–B · 109 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1YMS · X-ray crystallographic structure of CTX-M-9 beta-lactamase complexed with nafcinin-like… · 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 1YMS · PDBe 1YMS · UniProt Q9L5C8
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