Research workbench
Crystal structure of the mycobacterium tuberculosis pknb mutant kinase domain in complex with KT5720
Analyse Crystal structure of the mycobacterium tuberculosis pknb mutant kinase domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F69
- Type
- protein
- Length
- 553 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pknb
- EC
- 2.7.11.1
- UniProt
- P0A5S4
- Ligands
- XDR, SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pknb (EC 2.7.11.1) | protein | 270 | 39% helix, 21% strand | P0A5S4 |
| B | SERINE/THREONINE-protein kinase pknb (EC 2.7.11.1) | protein | 283 | 38% helix, 19% strand | P0A5S4 |
Ligands and binding sites
- XDR · hexyl (5S,6R,8R)-6-hydroxy-5-methyl-13-oxo-5,6,7,8-tetrahydro-13H-5,8-epoxy-4b,8a,14-triazadibenzo[b,h]cycloocta[1,2,3,4-jkl]c yclopenta[e]-as-indacene-6-carboxylate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.79 | 0.81 | 88 | XDR |
| 2 | 355 | 0.73 | 0.84 | 39 | XDR |
| 3 | 78 | 0.35 | 0.76 | 16 | empty |
| 4 | 61 | 0.28 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 954 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3F69 · Crystal structure of the Mycobacterium tuberculosis PknB mutant kinase domain in complex… · 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 P0A5S4
- Elsewhere: RCSB PDB 3F69 · PDBe 3F69 · UniProt P0A5S4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.