MolNFT v1 · #163368 · protein
The crystal structure of kanamycin B dioxygenase (kanj) from streptomyces kanamyceticus in complex with nickel and kanamycin B sulfate
6S0W: “The crystal structure of kanamycin B dioxygenase (kanj) from streptomyces kanamyceticus in complex with…”. X-ray diffraction, 3 ligands (9CS, NI, SO4). MolNFT v1 #163368 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6S0W
- Type
- protein
- Length
- 1,670 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- Q6L732
- Ligands
- 9CS, NI, SO4
Structure
x-ray diffraction · 6 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 275 | — | Q6L732 |
| B | — | protein | 282 | — | Q6L732 |
| C | — | protein | 277 | — | Q6L732 |
| D | — | protein | 279 | — | Q6L732 |
| E | — | protein | 274 | — | Q6L732 |
| F | — | protein | 283 | — | Q6L732 |
Ligands and binding sites
- 9CS · (1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside · ligand · 6 copies · chains A, B, C, D, E, F
- NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 19 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 6S0W · The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus… · the same entry in another collection · chain F against F, TM-score 1.00
- Q6L732 · AlphaFold monomer V2.0 prediction for kanamycin B dioxygenase (Q6L732) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 Q6L732
- Elsewhere: RCSB PDB 6S0W · PDBe 6S0W · UniProt Q6L732
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