MolNFT v1 · #109462 · protein
Crystal structure of the intracellular domain of the M. tuberculosis SER/THR kinase pkna
4X3F · SERINE/THREONINE-protein kinase pkna: “Crystal structure of the intracellular domain of the M. tuberculosis SER/THR kinase pkna”. X-ray diffraction, 7 pockets (best druggability 0.68). MolNFT v1 #109462 on GenesisL1: 3D structure…
- PDB
- 4X3F
- Type
- protein
- Length
- 831 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pkna
- EC
- 2.7.11.1
- UniProt
- P9WI83
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pkna (EC 2.7.11.1) | protein | 277 | 41% helix, 19% strand | P9WI83 |
| B | SERINE/THREONINE-protein kinase pkna (EC 2.7.11.1) | protein | 280 | 40% helix, 19% strand | P9WI83 |
| C | SERINE/THREONINE-protein kinase pkna (EC 2.7.11.1) | protein | 274 | 41% helix, 18% strand | P9WI83 |
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.68 | 0.81 | 44 | empty |
| 2 | 360 | 0.68 | 0.81 | 40 | empty |
| 3 | 431 | 0.67 | 0.79 | 54 | empty |
| 4 | 327 | 0.53 | 0.74 | 36 | empty |
| 5 | 174 | 0.51 | 0.78 | 35 | empty |
Interfaces
3 interfaces between chains.
- B–C · 533 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 100 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
- 4X3F · Crystal structure of the intracellular domain of the M. tuberculosis Ser/Thr kinase PknA · the same entry in another collection · chain A against A, TM-score 1.00
- P9WI83 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pkna (P9WI83) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P9WI83
- Elsewhere: RCSB PDB 4X3F · PDBe 4X3F · UniProt P9WI83
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