Research workbench
Oxidoreductase fragment of mouse QSOX1 in complex with a Fab fragment from an antibody targeting mouse and human QSOX1
Analyse Oxidoreductase fragment of mouse QSOX1 in complex with a Fab fragment from an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D96
- Type
- protein
- Length
- 1,328 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfhydryl oxidase 1; Light chain of Fab fragment from an antibody targeting mouse and…
- EC
- 1.8.3.2
- UniProt
- Q8BND5
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Sulfhydryl oxidase 1 (EC 1.8.3.2) | protein | 234 | 32% helix, 21% strand | Q8BND5 |
| I, B | Light chain of Fab fragment from an antibody targeting mouse and human QSOX1 | protein | 214 | 5% helix, 50% strand | — |
| J | Heavy chain of Fab fragment from an antibody targeting mouse and human QSOX1 | protein | 215 | 6% helix, 53% strand | — |
| A | Sulfhydryl oxidase 1 (EC 1.8.3.2) | protein | 237 | 32% helix, 20% strand | Q8BND5 |
| C | Heavy chain of Fab fragment from an antibody targeting mouse and human QSOX1 | protein | 214 | 4% helix, 53% strand | — |
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.69 | 0.97 | 22 | empty |
| 2 | 576 | 0.62 | 0.74 | 64 | empty |
| 3 | 315 | 0.59 | 0.77 | 62 | empty |
| 4 | 54 | 0.57 | 0.90 | 15 | empty |
| 5 | 239 | 0.53 | 0.76 | 39 | empty |
Interfaces
7 interfaces between chains.
- I–J · 1854 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1770 Ų buried · 18 hydrogen bonds · protein-protein
- D–J · 632 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 612 Ų buried · 2 hydrogen bonds · protein-protein
- D–B · 448 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5D96 · Oxidoreductase Fragment of Mouse QSOX1 in Complex with a FAb Fragment from an Antibody… · the same entry in another collection · chain C against C, TM-score 1.00
- Q8BND5 · AlphaFold monomer V2.0 prediction for sulfhydryl oxidase 1 (Q8BND5) · a predicted model of the same protein · chain A 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 5D96 · PDBe 5D96 · UniProt Q8BND5
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