Research workbench
Cryo-EM structure of human DUOX1-DUOXA1 in low-calcium state
Analyse Cryo-EM structure of human DUOX1-DUOXA1 in low-calcium state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D3E
- Type
- protein
- Length
- 3,304 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual oxidase 1; Isoform 2 of dual oxidase maturation factor 1
- EC
- 1.11.1.-, 1.6.3.1
- UniProt
- Q9NRD9, Q1HG43
- Ligands
- HEM, NDP, FAD, NAG, MAN, BMA, NA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dual oxidase 1 (EC 1.11.1.-, 1.6.3.1) | protein | 1380 | 46% helix, 13% strand | Q9NRD9 |
| B, D | Isoform 2 of dual oxidase maturation factor 1 | protein | 272 | 54% helix, 19% strand | Q1HG43 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, C
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, C
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains B, C, D, A
- MAN · alpha-D-mannopyranose · sugar · 14 copies · chains B, C, A, D
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, C, A, D
- NA · Sodium ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.87 | 0.89 | 89 | empty |
| 2 | 858 | 0.87 | 0.89 | 87 | empty |
| 3 | 914 | 0.84 | 0.86 | 101 | HEM, FAD |
| 4 | 377 | 0.84 | 0.92 | 45 | HEM |
| 5 | 922 | 0.83 | 0.85 | 98 | HEM, FAD |
Interfaces
5 interfaces between chains.
- B–C · 1689 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1687 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1606 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1596 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1412 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 7D3E · Cryo-EM structure of human DUOX1-DUOXA1 in low-calcium state · the same entry in another collection · chain D against D, TM-score 1.00
- Q1HG43 · AlphaFold monomer V2.0 prediction for dual oxidase maturation factor 1 (Q1HG43) · a predicted model of the same protein · chain B against A, TM-score 1.00
- Q9NRD9 · AlphaFold monomer V2.0 prediction for dual oxidase 1 (Q9NRD9) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q9NRD9
- Every structure of UniProt Q1HG43
- Elsewhere: RCSB PDB 7D3E · PDBe 7D3E · UniProt Q9NRD9 · UniProt Q1HG43
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