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Crystal structure of the S/T protein kinase pkng from corynebacterium glutamicum in complex with AMP-pnp
Analyse Crystal structure of the S/T protein kinase pkng from corynebacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MXB
- Type
- protein
- Length
- 1,327 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE protein kinases
- UniProt
- Q8NM29
- Ligands
- MAP, MG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE protein kinases | protein | 672 | 48% helix, 11% strand | Q8NM29 |
| B | SERINE/THREONINE protein kinases | protein | 655 | 49% helix, 11% strand | Q8NM29 |
Ligands and binding sites
- MAP · Magnesium-5'-adenyly-imido-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.73 | 0.76 | 89 | MAP, MG |
| 2 | 424 | 0.68 | 0.79 | 51 | MAP, MG |
| 3 | 484 | 0.67 | 0.79 | 57 | empty |
| 4 | 129 | 0.61 | 0.86 | 28 | empty |
| 5 | 142 | 0.61 | 0.85 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 661 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7MXB · Crystal structure of the S/T protein kinase PknG from Corynebacterium glutamicum in… · 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 Q8NM29
- Elsewhere: RCSB PDB 7MXB · PDBe 7MXB · UniProt Q8NM29
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