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The crystal structure of kanamycin B dioxygenase (kanj) from streptomyces kanamyceticus in complex with nickel, ribostamycin B and 2-oxoglutarate
Analyse The crystal structure of kanamycin B dioxygenase (kanj) from streptomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S0S
- Type
- protein
- Length
- 1,672 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
- AKG, RIO, NI, CL
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 5 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 | 283 | 26% helix, 23% strand | Q6L732 |
| C, F | Kanamycin B dioxygenase (EC 1.14.11.37) | protein | 277 | 26% helix, 24% strand | Q6L732 |
| D | Kanamycin B dioxygenase (EC 1.14.11.37) | protein | 279 | 26% helix, 25% strand | Q6L732 |
| E | Kanamycin B dioxygenase (EC 1.14.11.37) | protein | 274 | 27% helix, 24% strand | Q6L732 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 6 copies · chains A, B, C, D, E, F
- RIO · Ribostamycin · ligand · 6 copies · chains A, B, C, D, E, F
- NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 3 copies · chains B, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.69 | 0.77 | 64 | empty |
| 2 | 377 | 0.65 | 0.79 | 52 | NI, AKG, RIO |
| 3 | 304 | 0.63 | 0.80 | 47 | AKG, RIO |
| 4 | 299 | 0.62 | 0.79 | 46 | NI, AKG, RIO |
| 5 | 203 | 0.62 | 0.83 | 31 | AKG, RIO |
Interfaces
6 interfaces between chains.
- C–F · 585 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 530 Ų buried · 0 hydrogen bonds · protein-protein
- D–F · 205 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 156 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 100 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6S0S · 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 0.97
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 6S0S · PDBe 6S0S · UniProt Q6L732
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