Research workbench
GC1 beta-lactamase with a penem inhibitor
Analyse GC1 beta-lactamase with a penem inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ONH
- Type
- protein
- Length
- 363 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class C beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q59401
- Ligands
- WY4
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class C beta-lactamase (EC 3.5.2.6) | protein | 363 | 40% helix, 23% strand | Q59401 |
Ligands and binding sites
- WY4 · 7-(5,6-dihydro-8H-imidazo[2,1-c][1,4]oxazin-2-yl)-6-formyl-2,7-dihydro- [1,4]thiazepine-3-carboxylic acid · ligand · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.74 | 0.81 | 72 | WY4, GOL |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1ONH · GC1 beta-lactamase with a penem inhibitor · 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 Q59401
- Elsewhere: RCSB PDB 1ONH · PDBe 1ONH · UniProt Q59401
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