Research workbench
Crystal structure of xanthine dehydrogenase family protein
Analyse Crystal structure of xanthine dehydrogenase family protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DQX
- Type
- protein
- Length
- 2,435 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-hydroxypseudooxynicotine dehydrogenase complex subunit gamma…
- EC
- 1.5.99.14
- UniProt
- Q933N0, O87681, O87682
- Ligands
- FES, MCN, FAD, MO
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-hydroxypseudooxynicotine dehydrogenase complex subunit gamma (EC 1.5.99.14) | protein | 765 | 24% helix, 17% strand | Q933N0 |
| B | 6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha (EC 1.5.99.14) | protein | 287 | 29% helix, 26% strand | O87681 |
| C, F | 6-hydroxypseudooxynicotine dehydrogenase complex subunit beta (EC 1.5.99.14) | protein | 160 | 35% helix, 18% strand | O87682 |
| E | 6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha (EC 1.5.99.14) | protein | 293 | 28% helix, 24% strand | O87681 |
| D | 6-hydroxypseudooxynicotine dehydrogenase complex subunit gamma (EC 1.5.99.14) | protein | 770 | 24% helix, 19% strand | Q933N0 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains C, A, F, D
- MCN · Pterin cytosine dinucleotide · ligand · 2 copies · chains A, C, F, D
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains B, C, E, F, D
- MO · Molybdenum atom · metal · 2 copies · chains A, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.89 | 0.91 | 114 | MCN, MO |
| 2 | 833 | 0.86 | 0.89 | 116 | empty |
| 3 | 1000 | 0.86 | 0.87 | 108 | MCN, MO |
| 4 | 812 | 0.85 | 0.87 | 94 | FAD |
| 5 | 657 | 0.83 | 0.88 | 83 | empty |
Interfaces
9 interfaces between chains.
- F–D · 2253 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 2232 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 2102 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1276 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1268 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 7DQX · Crystal structure of xanthine dehydrogenase family protein · the same entry in another collection · chain D against D, TM-score 1.00
- O87682 · AlphaFold monomer V2.0 prediction for 6-hydroxypseudooxynicotine dehydrogenase complex… · a predicted model of the same protein · chain C against A, TM-score 0.98
- O87681 · AlphaFold monomer V2.0 prediction for 6-hydroxypseudooxynicotine dehydrogenase complex… · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q933N0 · AlphaFold monomer V2.0 prediction for 6-hydroxypseudooxynicotine dehydrogenase complex… · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q933N0
- Every structure of UniProt O87681
- Every structure of UniProt O87682
- Elsewhere: RCSB PDB 7DQX · PDBe 7DQX · UniProt Q933N0 · UniProt O87681 · UniProt O87682
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