MolNFT v1 · #63319 · protein
Crystal structure of the mycobacterium tuberculosis pknb mutant kinase domain in complex with KT5720
3F69 · SERINE/THREONINE-protein kinase pknb: “Crystal structure of the mycobacterium tuberculosis pknb mutant kinase domain in complex with KT5720”. X-ray diffraction, 2 ligands (XDR, SO4), 4 pockets (best druggability 0.79). MolNFT v1…
- 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
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