Research workbench
Structure of deoxyadenosine kinase from M.MYCOIDES with bound datp
Analyse Structure of deoxyadenosine kinase from M.MYCOIDES with bound datp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JAS
- Type
- protein
- Length
- 1,161 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyguanosine kinase
- EC
- 2.7.1.113
- UniProt
- Q93IG4
- Ligands
- DTP, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 57% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyguanosine kinase (EC 2.7.1.113) | protein | 194 | 57% helix, 12% strand | Q93IG4 |
| B | Deoxyguanosine kinase (EC 2.7.1.113) | protein | 193 | 58% helix, 12% strand | Q93IG4 |
| C | Deoxyguanosine kinase (EC 2.7.1.113) | protein | 195 | 55% helix, 13% strand | Q93IG4 |
| D | Deoxyguanosine kinase (EC 2.7.1.113) | protein | 192 | 55% helix, 12% strand | Q93IG4 |
| E | Deoxyguanosine kinase (EC 2.7.1.113) | protein | 194 | 58% helix, 12% strand | Q93IG4 |
| F | Deoxyguanosine kinase (EC 2.7.1.113) | protein | 193 | 57% helix, 11% strand | Q93IG4 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.86 | 0.87 | 102 | empty |
| 2 | 255 | 0.74 | 0.88 | 31 | DTP, MG |
| 3 | 563 | 0.73 | 0.81 | 67 | DTP, MG |
| 4 | 263 | 0.72 | 0.86 | 31 | MG, DTP |
| 5 | 262 | 0.71 | 0.86 | 37 | DTP, MG |
Interfaces
8 interfaces between chains.
- A–B · 1086 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1055 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1001 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 556 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 528 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2JAS · Structure of deoxyadenosine kinase from M.mycoides with bound dATP · 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 2JAS · PDBe 2JAS · UniProt Q93IG4
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