Research workbench
Structure of bacterial polynucleotide kinase bound to GTP and RNA
Analyse Structure of bacterial polynucleotide kinase bound to GTP and RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QM6
- Type
- protein + RNA
- Length
- 350 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallophosphoesterase; RNA
- UniProt
- A3DJ38
- Ligands
- GTP, NA, MG, PO4
- Pockets
- 5 · best druggability 0.60
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 | RNA | rna | 4 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C, B, D
- NA · Sodium ion · metal · 5 copies · chains A, B, D
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, C
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 | 170 | 0.60 | 0.83 | 18 | empty |
| 2 | 111 | 0.42 | 0.77 | 17 | empty |
| 3 | 124 | 0.42 | 0.76 | 27 | GTP, MG |
| 4 | 69 | 0.38 | 0.79 | 19 | GTP, MG |
| 5 | 62 | 0.38 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 886 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 679 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 675 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 4QM6 · Structure of bacterial polynucleotide kinase bound to GTP and RNA · 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 4QM6 · PDBe 4QM6 · UniProt A3DJ38
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