MolNFT v1 · #163366 · protein
The crystal structure of kanamycin B dioxygenase (kanj) from streptomyces kanamyceticus in complex with nickel and 2-oxoglutarate
6S0U: “The crystal structure of kanamycin B dioxygenase (kanj) from streptomyces kanamyceticus in complex with…”. X-ray diffraction, 4 ligands (AKG, NI, NA), 14 pockets (best druggability 0.69). MolNFT v1 #163366 on GenesisL1: 3D…
- PDB
- 6S0U
- Type
- protein
- Length
- 1,655 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, NI, NA, CL
- Pockets
- 14 · 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 | 276 | 26% helix, 24% strand | Q6L732 |
| B, E | Kanamycin B dioxygenase (EC 1.14.11.37) | protein | 275 | 27% helix, 24% strand | Q6L732 |
| C | Kanamycin B dioxygenase (EC 1.14.11.37) | protein | 276 | 26% helix, 24% strand | Q6L732 |
| D | Kanamycin B dioxygenase (EC 1.14.11.37) | protein | 278 | 26% helix, 25% strand | Q6L732 |
| F | Kanamycin B dioxygenase (EC 1.14.11.37) | protein | 275 | 27% helix, 24% strand | Q6L732 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 6 copies · chains A, B, C, D, E, F
- NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · chains E
- CL · Chloride ion · ion · 2 copies · chains C, F, E
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.69 | 0.77 | 58 | empty |
| 2 | 363 | 0.65 | 0.80 | 51 | AKG |
| 3 | 292 | 0.63 | 0.80 | 48 | AKG, NI |
| 4 | 327 | 0.62 | 0.79 | 46 | AKG, NI |
| 5 | 209 | 0.61 | 0.82 | 36 | AKG |
Interfaces
7 interfaces between chains.
- C–F · 548 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 541 Ų buried · 0 hydrogen bonds · protein-protein
- D–F · 216 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 178 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 128 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6S0U · 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 A 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 6S0U · PDBe 6S0U · UniProt Q6L732
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