Research workbench
Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA
Analyse Structure of bacterial polynucleotide kinase product complex bound to GDP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MDE
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallophosphoesterase; DNA (5'-D(P*CP*CP*TP*GP*T)-3')
- UniProt
- A3DJ38
- Ligands
- GDP, MG
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallophosphoesterase | protein | 171 | 50% helix, 22% strand | A3DJ38 |
| C, D | DNA (5'-D(P*CP*CP*TP*GP*T)-3') | dna | 5 | — | — |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.61 | 0.83 | 21 | empty |
| 2 | 84 | 0.39 | 0.78 | 17 | empty |
| 3 | 78 | 0.38 | 0.77 | 16 | empty |
| 4 | 56 | 0.30 | 0.76 | 13 | GDP |
| 5 | 52 | 0.29 | 0.76 | 12 | GDP |
Interfaces
3 interfaces between chains.
- A–B · 852 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 744 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 719 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 4MDE · Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA · 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 A3DJ38
- Elsewhere: RCSB PDB 4MDE · PDBe 4MDE · UniProt A3DJ38
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