MolNFT v1 · #41021 · protein
Structure of deoxyadenosine kinase from M.MYCOIDES with products dcmp and a flexible dcdp bound
2JAT · Deoxyguanosine kinase: “Structure of deoxyadenosine kinase from M.MYCOIDES with products dcmp and a flexible dcdp bound”. X-ray diffraction, 3 ligands (POP, DCM, MG), 5 pockets (best druggability 0.75). MolNFT v1 #41021 on…
- PDB
- 2JAT
- Type
- protein
- Length
- 382 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyguanosine kinase
- EC
- 2.7.1.113
- UniProt
- Q93IG4
- Ligands
- POP, DCM, MG
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyguanosine kinase (EC 2.7.1.113) | protein | 190 | 56% helix, 12% strand | Q93IG4 |
| B | Deoxyguanosine kinase (EC 2.7.1.113) | protein | 192 | 56% helix, 12% strand | Q93IG4 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- DCM · 2'-deoxycytidine-5'-monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.75 | 0.88 | 31 | MG, POP, DCM |
| 2 | 324 | 0.74 | 0.86 | 37 | MG, POP, DCM |
| 3 | 82 | 0.33 | 0.74 | 15 | empty |
| 4 | 59 | 0.31 | 0.75 | 13 | empty |
| 5 | 70 | 0.28 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 951 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2JAT · Structure of deoxyadenosine kinase from M.mycoides with products dcmp and a flexible dcdp… · 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 Q93IG4
- Elsewhere: RCSB PDB 2JAT · PDBe 2JAT · UniProt Q93IG4
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