Research workbench
Structure of burkholderia thailandensis nucleoside kinase (bthnk) in complex with ADP-mizoribine
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
- 3B1N
- Type
- protein
- Length
- 631 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribokinase, putative
- EC
- 2.7.1.143
- UniProt
- Q2SZE4
- Ligands
- MZR, ADP, NA
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribokinase, putative (EC 2.7.1.143) | protein | 311 | 41% helix, 24% strand | Q2SZE4 |
| B | Ribokinase, putative (EC 2.7.1.143) | protein | 320 | 39% helix, 23% strand | Q2SZE4 |
Ligands and binding sites
- MZR · 5-hydroxy-1-(beta-D-ribofuranosyl)-1H-imidazole-4-carboxamide · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.82 | 0.89 | 76 | MZR, ADP |
| 2 | 363 | 0.81 | 0.90 | 58 | MZR, ADP |
| 3 | 162 | 0.52 | 0.79 | 29 | empty |
| 4 | 73 | 0.46 | 0.82 | 18 | empty |
| 5 | 66 | 0.43 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2311 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 3B1N · Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with… · 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 3B1N · PDBe 3B1N · UniProt Q2SZE4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.