MolNFT v1 · #76194 · protein
C72S/C353S mutant of trypanosoma brucei qsox containing an interdomain disulfide
3QD9 · Qsox from trypanosoma brucei (tbqsox): “C72S/C353S mutant of trypanosoma brucei qsox containing an interdomain disulfide”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.84). MolNFT v1 #76194 on GenesisL1: 3D…
- PDB
- 3QD9
- Type
- protein
- Length
- 1,547 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Qsox from trypanosoma brucei (tbqsox)
- EC
- 1.8.3.2
- UniProt
- Q585M6
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Qsox from trypanosoma brucei (tbqsox) (EC 1.8.3.2) | protein | 388 | 46% helix, 8% strand | Q585M6 |
| B | Qsox from trypanosoma brucei (tbqsox) (EC 1.8.3.2) | protein | 390 | 46% helix, 9% strand | Q585M6 |
| C | Qsox from trypanosoma brucei (tbqsox) (EC 1.8.3.2) | protein | 385 | 47% helix, 8% strand | Q585M6 |
| D | Qsox from trypanosoma brucei (tbqsox) (EC 1.8.3.2) | protein | 384 | 47% helix, 9% strand | Q585M6 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.84 | 0.89 | 52 | FAD |
| 2 | 606 | 0.84 | 0.88 | 53 | FAD |
| 3 | 648 | 0.83 | 0.87 | 55 | FAD |
| 4 | 971 | 0.82 | 0.83 | 83 | FAD |
| 5 | 443 | 0.69 | 0.80 | 56 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1009 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 961 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 634 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 627 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 61 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 3QD9 · C72S/C353S mutant of Trypanosoma brucei QSOX containing an interdomain disulfide · 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 Q585M6
- Elsewhere: RCSB PDB 3QD9 · PDBe 3QD9 · UniProt Q585M6
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