MolNFT v1 · #37230 · protein
Catalytic domain of protein kinase pknb from mycobacterium tuberculosis in complex with mitoxantrone
2FUM · Probable SERINE/THREONINE-protein kinase pknb: “Catalytic domain of protein kinase pknb from mycobacterium tuberculosis in complex with mitoxantrone”. X-ray diffraction, 1 ligand (MIX), 11 pockets (best druggability 0.69). MolNFT v1…
- 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
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