MolNFT v1 · #163367 · protein
The crystal structure of kanamycin B dioxygenase (kanj) from streptomyces kanamyceticus in complex with nickel, neamine and sulfate
6S0V: “The crystal structure of kanamycin B dioxygenase (kanj) from streptomyces kanamyceticus in complex with…”. X-ray diffraction, 3 ligands (XXX, NI, SO4), 15 pockets (best druggability 0.75). MolNFT v1 #163367 on GenesisL1: 3D…
- PDB
- 6S0V
- Type
- protein
- Length
- 1,682 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kanamycin B dioxygenase
- EC
- 1.14.11.37
- UniProt
- Q6L732
- Ligands
- XXX, NI, SO4
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 26% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kanamycin B dioxygenase (EC 1.14.11.37) | protein | 282 | 26% helix, 23% strand | Q6L732 |
| B | Kanamycin B dioxygenase (EC 1.14.11.37) | protein | 284 | 24% helix, 23% strand | Q6L732 |
| C | Kanamycin B dioxygenase (EC 1.14.11.37) | protein | 278 | 26% helix, 24% strand | Q6L732 |
| D | Kanamycin B dioxygenase (EC 1.14.11.37) | protein | 284 | 26% helix, 24% strand | Q6L732 |
| E | Kanamycin B dioxygenase (EC 1.14.11.37) | protein | 271 | 28% helix, 24% strand | Q6L732 |
| F | Kanamycin B dioxygenase (EC 1.14.11.37) | protein | 283 | 27% helix, 23% strand | Q6L732 |
Ligands and binding sites
- XXX · (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 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 · 18 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.75 | 0.89 | 44 | SO4, XXX |
| 2 | 251 | 0.72 | 0.87 | 49 | NI, SO4, XXX |
| 3 | 686 | 0.69 | 0.77 | 59 | empty |
| 4 | 378 | 0.65 | 0.79 | 53 | NI, SO4, XXX |
| 5 | 310 | 0.63 | 0.80 | 48 | SO4, XXX |
Interfaces
7 interfaces between chains.
- C–F · 553 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 532 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 187 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 125 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 109 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6S0V · 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 6S0V · PDBe 6S0V · UniProt Q6L732
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