Research workbench
Human milk xanthine oxidoreductase
Analyse Human milk xanthine oxidoreductase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CKJ
- Type
- protein
- Length
- 5,119 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xanthine oxidoreductase
- EC
- 1.1.1.204, 1.2.3.2, 1.17.3.2
- UniProt
- P47989
- Ligands
- FES, FAD, PO4
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xanthine oxidoreductase (EC 1.1.1.204, 1.2.3.2, 1.17.3.2) | protein | 1264 | 30% helix, 22% strand | P47989 |
| B | Xanthine oxidoreductase (EC 1.1.1.204, 1.2.3.2, 1.17.3.2) | protein | 1289 | 29% helix, 22% strand | P47989 |
| C | Xanthine oxidoreductase (EC 1.1.1.204, 1.2.3.2, 1.17.3.2) | protein | 1283 | 29% helix, 22% strand | P47989 |
| D | Xanthine oxidoreductase (EC 1.1.1.204, 1.2.3.2, 1.17.3.2) | protein | 1283 | 29% helix, 22% strand | P47989 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 8 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- ACY · Acetic acid · additive · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.90 | 0.92 | 149 | empty |
| 2 | 868 | 0.85 | 0.87 | 98 | FAD |
| 3 | 584 | 0.84 | 0.89 | 73 | empty |
| 4 | 1010 | 0.84 | 0.85 | 111 | FAD |
| 5 | 239 | 0.83 | 0.96 | 46 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2819 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 723 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 265 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
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 P47989
- Elsewhere: RCSB PDB 2CKJ · PDBe 2CKJ · UniProt P47989
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