Research workbench
Crystal structure of Q4D6Q6, a conserved kinetoplastid-specific protein from trypanosoma cruzi
Analyse Crystal structure of Q4D6Q6, a conserved kinetoplastid-specific protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XYB
- Type
- protein
- Length
- 421 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q4D6Q6
- Ligands
- MG, K, IOD, CL
- Pockets
- 9 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 106 | 25% helix, 40% strand | Q4D6Q6 |
| B | Uncharacterized protein | protein | 102 | 26% helix, 41% strand | Q4D6Q6 |
| C | Uncharacterized protein | protein | 108 | 25% helix, 39% strand | Q4D6Q6 |
| D | Uncharacterized protein | protein | 105 | 30% helix, 36% strand | Q4D6Q6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- K · Potassium ion · metal · chains A, B, C, D
- IOD · Iodide ion · ion · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.51 | 0.78 | 33 | empty |
| 2 | 152 | 0.49 | 0.78 | 39 | empty |
| 3 | 148 | 0.48 | 0.78 | 34 | empty |
| 4 | 176 | 0.48 | 0.77 | 36 | empty |
| 5 | 159 | 0.45 | 0.75 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1137 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1041 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 991 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 945 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 34 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 6XYB · Crystal structure of Q4D6Q6, a conserved kinetoplastid-specific protein from Trypanosoma… · 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 Q4D6Q6
- Elsewhere: RCSB PDB 6XYB · PDBe 6XYB · UniProt Q4D6Q6
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