Research workbench
Structure of bacterial polynucleotide kinase bound to GTP and pdna
Analyse Structure of bacterial polynucleotide kinase bound to GTP and pdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QM7
- Type
- protein + DNA
- Length
- 345 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallophosphoesterase; DNA
- UniProt
- A3DJ38
- Ligands
- GTP, 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 | DNA | dna | 3 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.61 | 0.83 | 20 | empty |
| 2 | 239 | 0.55 | 0.77 | 38 | GTP, MG |
| 3 | 162 | 0.53 | 0.80 | 30 | GTP, MG |
| 4 | 110 | 0.42 | 0.78 | 19 | empty |
| 5 | 63 | 0.33 | 0.77 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 912 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 570 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4QM7 · Structure of bacterial polynucleotide kinase bound to GTP and pDNA · 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 4QM7 · PDBe 4QM7 · UniProt A3DJ38
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