Research workbench
Crystal structure of mycobacterium tuberculosis pkni kinase domain, C20A_R136N double mutant
Analyse Crystal structure of mycobacterium tuberculosis pkni kinase domain, C20A_R136N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M09
- Type
- protein
- Length
- 491 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
- NA
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pkni (EC 2.7.11.1) | protein | 246 | 41% helix, 22% strand | P9WI69 |
| B | SERINE/THREONINE-protein kinase pkni (EC 2.7.11.1) | protein | 245 | 42% helix, 20% strand | P9WI69 |
Ligands and binding sites
- NA · Sodium 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.64 | 0.80 | 34 | empty |
| 2 | 284 | 0.58 | 0.77 | 29 | empty |
| 3 | 90 | 0.36 | 0.75 | 12 | empty |
| 4 | 74 | 0.33 | 0.75 | 18 | empty |
| 5 | 81 | 0.32 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 407 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5M09 · Crystal structure of Mycobacterium tuberculosis PknI kinase domain, C20A_R136N double… · 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 5M09 · PDBe 5M09 · UniProt P9WI69
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