Research workbench
Crystal structure of the kinetoplastid kinetochore protein trypanosoma brucei KKT3 divergent polo-box domain
Analyse Crystal structure of the kinetoplastid kinetochore protein trypanosoma brucei… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8A0K
- Type
- protein
- Length
- 815 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein kinase, putative
- UniProt
- Q38DT1
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein kinase, putative | protein | 206 | 19% helix, 32% strand | Q38DT1 |
| B | Protein kinase, putative | protein | 206 | 19% helix, 31% strand | Q38DT1 |
| C | Protein kinase, putative | protein | 200 | 22% helix, 33% strand | Q38DT1 |
| D | Protein kinase, putative | protein | 203 | 20% helix, 32% strand | Q38DT1 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.78 | 0.79 | 77 | PEG |
| 2 | 333 | 0.55 | 0.75 | 52 | empty |
| 3 | 187 | 0.47 | 0.76 | 31 | empty |
| 4 | 131 | 0.44 | 0.77 | 30 | empty |
| 5 | 50 | 0.43 | 0.83 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–C · 636 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 549 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 54 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 8A0K · crystal structure of the kinetoplastid kinetochore protein Trypanosoma brucei KKT3… · 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 Q38DT1
- Elsewhere: RCSB PDB 8A0K · PDBe 8A0K · UniProt Q38DT1
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