MolNFT v1 · #128986 · protein
Crystal structure of the BC1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide
5O6Y: “Crystal structure of the BC1960 peptidoglycan N-acetylglucosamine deacetylase in complex with…”. X-ray diffraction, 5 ligands (5YA, NA, ZN). MolNFT v1 #128986 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5O6Y
- Type
- protein
- Length
- 856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- Q81EK9
- Ligands
- 5YA, NA, ZN, SO4, CL
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 214 | — | Q81EK9 |
| B, C, D | — | protein | 214 | — | Q81EK9 |
Ligands and binding sites
- 5YA · 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 21 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains B, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, B, C, D
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 2 copies · chains A, C, D
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5O6Y · Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q81EK9 · AlphaFold monomer V2.0 prediction for peptidoglycan-N- acetylglucosamine deacetylase… · a predicted model of the same protein · 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 Q81EK9
- Elsewhere: RCSB PDB 5O6Y · PDBe 5O6Y · UniProt Q81EK9
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