MolNFT v1 · #4150 · protein
Deoxynucleoside monophosphate kinase complexed with deoxy-gmp
1DEK: “Deoxynucleoside monophosphate kinase complexed with deoxy-gmp”. X-ray diffraction, 2 ligands (DGP, MG), 6 pockets (best druggability 0.69). MolNFT v1 #4150 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1DEK
- Type
- protein
- Length
- 472 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside monophosphate kinase
- EC
- 2.7.4.13
- UniProt
- P04531
- Ligands
- DGP, MG
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside monophosphate kinase (EC 2.7.4.13) | protein | 241 | 46% helix, 12% strand | P04531 |
| B | Deoxynucleoside monophosphate kinase (EC 2.7.4.13) | protein | 231 | 48% helix, 13% strand | P04531 |
Ligands and binding sites
- DGP · 2'-deoxyguanosine-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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.69 | 0.88 | 28 | DGP |
| 2 | 225 | 0.53 | 0.77 | 25 | DGP |
| 3 | 71 | 0.47 | 0.83 | 22 | empty |
| 4 | 154 | 0.46 | 0.76 | 23 | empty |
| 5 | 152 | 0.45 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 906 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 1DEK · Deoxynucleoside monophosphate kinase complexed with deoxy-gmp · 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 P04531
- Elsewhere: RCSB PDB 1DEK · PDBe 1DEK · UniProt P04531
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