MolNFT v1 · #143543 · protein
Dual inhibition of the essential protein kinases a and B in mycobacterium tuberculosis
6B2Q · SERINE/THREONINE-protein kinase pkna: “Dual inhibition of the essential protein kinases a and B in mycobacterium tuberculosis”. X-ray diffraction, 2 ligands (CJJ, 0BD), 9 pockets (best druggability 0.65). MolNFT v1 #143543 on…
- PDB
- 6B2Q
- Type
- protein
- Length
- 1,054 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pkna
- EC
- 2.7.11.1
- UniProt
- A5TY85
- Ligands
- CJJ, 0BD
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pkna (EC 2.7.11.1) | protein | 262 | 39% helix, 19% strand | A5TY85 |
| B | SERINE/THREONINE-protein kinase pkna (EC 2.7.11.1) | protein | 267 | 39% helix, 18% strand | A5TY85 |
| C | SERINE/THREONINE-protein kinase pkna (EC 2.7.11.1) | protein | 265 | 38% helix, 19% strand | A5TY85 |
| D | SERINE/THREONINE-protein kinase pkna (EC 2.7.11.1) | protein | 260 | 41% helix, 18% strand | A5TY85 |
Ligands and binding sites
- CJJ · 5-{5-chloro-4-[(5-cyclopropyl-1H-pyrazol-3-yl) amino]pyrimidin-2-yl}thiophene-2-sulfonamide · ligand · 4 copies · chains A, B, C, D
- 0BD · 3-methyl-1-(2-methylpropyl)butyl 4-O-beta-L-gulopyranosyl-beta-D-glucopyranoside · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.65 | 0.82 | 43 | CJJ |
| 2 | 445 | 0.64 | 0.77 | 56 | empty |
| 3 | 233 | 0.63 | 0.82 | 35 | CJJ |
| 4 | 246 | 0.62 | 0.81 | 39 | CJJ |
| 5 | 407 | 0.61 | 0.77 | 48 | empty |
Interfaces
3 interfaces between chains.
- A–D · 839 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 838 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 228 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6B2Q · Dual Inhibition of the Essential Protein Kinases A and B in Mycobacterium tuberculosis · the same entry in another collection · chain D against D, TM-score 1.00
- A5TY85 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pkna (A5TY85) · a predicted model of the same protein · chain D 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 A5TY85
- Elsewhere: RCSB PDB 6B2Q · PDBe 6B2Q · UniProt A5TY85
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