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Structure of burkholderia thailandensis nucleoside kinase (bthnk) in complex with inosine
Analyse Structure of burkholderia thailandensis nucleoside kinase (bthnk) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B1Q
- Type
- protein
- Length
- 1,821 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribokinase, putative
- EC
- 2.7.1.143
- UniProt
- Q2SZE4
- Ligands
- NOS, NA
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribokinase, putative (EC 2.7.1.143) | protein | 303 | 42% helix, 26% strand | Q2SZE4 |
| B, E | Ribokinase, putative (EC 2.7.1.143) | protein | 306 | 41% helix, 26% strand | Q2SZE4 |
| C | Ribokinase, putative (EC 2.7.1.143) | protein | 305 | 42% helix, 26% strand | Q2SZE4 |
| D | Ribokinase, putative (EC 2.7.1.143) | protein | 303 | 41% helix, 26% strand | Q2SZE4 |
| F | Ribokinase, putative (EC 2.7.1.143) | protein | 298 | 42% helix, 27% strand | Q2SZE4 |
Ligands and binding sites
- NOS · Inosine · ligand · 6 copies · chains A, F, B, D, C, E
- NA · Sodium ion · metal · 15 copies · chains A, F, B, C, D, E
- ACT · Acetate ion · additive · 16 copies · chains A, F, B, C, E, D
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 6 copies · chains A, B, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.83 | 0.84 | 114 | P33, NOS, ACT, NA |
| 2 | 880 | 0.82 | 0.84 | 89 | NOS, ACT, NA |
| 3 | 928 | 0.81 | 0.82 | 82 | NOS, ACT |
| 4 | 896 | 0.80 | 0.82 | 89 | NOS, ACT, NA |
| 5 | 531 | 0.79 | 0.86 | 63 | NOS, ACT, NA |
Interfaces
9 interfaces between chains.
- C–E · 1572 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1289 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 1236 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 554 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 548 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3B1Q · Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with inosine · the same entry in another collection · 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 Q2SZE4
- Elsewhere: RCSB PDB 3B1Q · PDBe 3B1Q · UniProt Q2SZE4
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