Research workbench
Catalytic domain of protein kinase pknb from mycobacterium tuberculosis in complex with mitoxantrone
Analyse Catalytic domain of protein kinase pknb from mycobacterium tuberculosis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FUM
- Type
- protein
- Length
- 1,037 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable SERINE/THREONINE-protein kinase pknb
- EC
- 2.7.1.37
- UniProt
- P0A5S4
- Ligands
- MIX
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable SERINE/THREONINE-protein kinase pknb (EC 2.7.1.37) | protein | 263 | 41% helix, 22% strand | P0A5S4 |
| B | Probable SERINE/THREONINE-protein kinase pknb (EC 2.7.1.37) | protein | 262 | 42% helix, 22% strand | P0A5S4 |
| C | Probable SERINE/THREONINE-protein kinase pknb (EC 2.7.1.37) | protein | 254 | 40% helix, 21% strand | P0A5S4 |
| D | Probable SERINE/THREONINE-protein kinase pknb (EC 2.7.1.37) | protein | 258 | 40% helix, 20% strand | P0A5S4 |
Ligands and binding sites
- MIX · 1,4-dihydroxy-5,8-bis({2-[(2-hydroxyethyl) amino]ethyl}amino)-9,10-anthracenedione · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.69 | 0.85 | 33 | MIX |
| 2 | 507 | 0.67 | 0.78 | 48 | empty |
| 3 | 378 | 0.67 | 0.80 | 42 | empty |
| 4 | 516 | 0.66 | 0.77 | 56 | empty |
| 5 | 194 | 0.64 | 0.84 | 32 | MIX |
Interfaces
4 interfaces between chains.
- C–D · 854 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 847 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 417 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 248 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2FUM · Catalytic domain of protein kinase PknB from Mycobacterium tuberculosis in complex with… · the same entry in another collection · chain D against D, 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 2FUM · PDBe 2FUM · UniProt P0A5S4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.