Research workbench
Structure of bacterial polynucleotide kinase michaelis complex bound to GTP and DNA
Analyse Structure of bacterial polynucleotide kinase michaelis complex bound to GTP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MDF
- Type
- protein + DNA
- Length
- 351 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallophosphoesterase; DNA (5'-D(*CP*CP*TP*GP*T)-3')
- UniProt
- A3DJ38
- Ligands
- GTP, MG
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallophosphoesterase | protein | 171 | 51% helix, 22% strand | A3DJ38 |
| C | DNA (5'-D(*CP*CP*TP*GP*T)-3') | dna | 5 | — | — |
| D | DNA (5'-D(*CP*CP*TP*GP*T)-3') | dna | 4 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CIT · Citric acid · additive · chains A
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 | 185 | 0.62 | 0.83 | 20 | empty |
| 2 | 96 | 0.41 | 0.77 | 17 | empty |
| 3 | 71 | 0.39 | 0.80 | 22 | GTP, MG |
| 4 | 66 | 0.37 | 0.79 | 15 | empty |
| 5 | 79 | 0.36 | 0.77 | 23 | GTP, MG |
Interfaces
3 interfaces between chains.
- A–B · 854 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 678 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 654 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 4MDF · Structure of bacterial polynucleotide kinase Michaelis complex bound to GTP 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 4MDF · PDBe 4MDF · UniProt A3DJ38
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