MolNFT v1 · #79507 · protein
C76A/C455S mutant of mouse QSOX1 containing an interdomain disulfide
3T59 · Sulfhydryl oxidase 1: “C76A/C455S mutant of mouse QSOX1 containing an interdomain disulfide”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.85). MolNFT v1 #79507 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3T59
- Type
- protein
- Length
- 2,003 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfhydryl oxidase 1
- EC
- 1.8.3.2
- UniProt
- Q8BND5
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sulfhydryl oxidase 1 (EC 1.8.3.2) | protein | 501 | 45% helix, 12% strand | Q8BND5 |
| B | Sulfhydryl oxidase 1 (EC 1.8.3.2) | protein | 504 | 46% helix, 13% strand | Q8BND5 |
| C | Sulfhydryl oxidase 1 (EC 1.8.3.2) | protein | 500 | 46% helix, 12% strand | Q8BND5 |
| D | Sulfhydryl oxidase 1 (EC 1.8.3.2) | protein | 498 | 45% helix, 10% strand | Q8BND5 |
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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.85 | 0.89 | 68 | FAD |
| 2 | 568 | 0.84 | 0.90 | 62 | FAD |
| 3 | 498 | 0.84 | 0.90 | 70 | FAD |
| 4 | 563 | 0.83 | 0.88 | 65 | FAD |
| 5 | 690 | 0.68 | 0.76 | 79 | empty |
Interfaces
5 interfaces between chains.
- B–C · 790 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 739 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 204 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 145 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 144 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3T59 · C76A/C455S mutant of mouse QSOX1 containing an interdomain disulfide · the same entry in another collection · chain D against D, TM-score 1.00
- Q8BND5 · AlphaFold monomer V2.0 prediction for sulfhydryl oxidase 1 (Q8BND5) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q8BND5
- Elsewhere: RCSB PDB 3T59 · PDBe 3T59 · UniProt Q8BND5
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