Research workbench
Crystal structure of mycobacterium tuberculosis pkni kinase domain
Analyse Crystal structure of mycobacterium tuberculosis pkni kinase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M06
- Type
- protein
- Length
- 493 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pkni
- EC
- 2.7.11.1
- UniProt
- P9WI69
- Ligands
- ADP, CA
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pkni (EC 2.7.11.1) | protein | 245 | 41% helix, 20% strand | P9WI69 |
| B | SERINE/THREONINE-protein kinase pkni (EC 2.7.11.1) | protein | 248 | 41% helix, 20% strand | P9WI69 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.74 | 0.79 | 59 | ADP, CA |
| 2 | 373 | 0.63 | 0.78 | 33 | empty |
| 3 | 92 | 0.40 | 0.77 | 21 | empty |
| 4 | 75 | 0.37 | 0.77 | 16 | empty |
| 5 | 52 | 0.35 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 297 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5M06 · Crystal structure of Mycobacterium tuberculosis PknI kinase domain · the same entry in another collection · chain A against A, TM-score 1.00
- P9WI69 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pkni (P9WI69) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P9WI69
- Elsewhere: RCSB PDB 5M06 · PDBe 5M06 · UniProt P9WI69
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