MolNFT v1 · #58376 · protein
Structure of burkholderia thailandensis nucleoside kinase (bthnk) in complex with AMP-mg-AMP
3B1R · Ribokinase, putative: “Structure of burkholderia thailandensis nucleoside kinase (bthnk) in complex with AMP-mg-AMP”. X-ray diffraction, 2 ligands (AMP, MG), 15 pockets (best druggability 0.83). MolNFT v1 #58376 on GenesisL1: 3D…
- PDB
- 3B1R
- Type
- protein
- Length
- 1,860 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
- AMP, MG
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Ribokinase, putative (EC 2.7.1.143) | protein | 310 | 40% helix, 23% strand | Q2SZE4 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 12 copies · chains A, D, B, E, C, F
- MG · Magnesium ion · metal · 7 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.83 | 0.90 | 71 | AMP, MG |
| 2 | 445 | 0.82 | 0.90 | 73 | AMP, MG |
| 3 | 445 | 0.82 | 0.89 | 73 | AMP, MG |
| 4 | 380 | 0.82 | 0.91 | 62 | AMP, MG |
| 5 | 394 | 0.81 | 0.90 | 67 | AMP, MG |
Interfaces
5 interfaces between chains.
- B–E · 2347 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 2297 Ų buried · 36 hydrogen bonds · protein-protein
- C–F · 2248 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 436 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 322 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3B1R · 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 3B1R · PDBe 3B1R · UniProt Q2SZE4
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