Research workbench
Crystal structure of bovine xanthine oxidase in complex with indole-3- aldehyde
Analyse Crystal structure of bovine xanthine oxidase in complex with indole-3- aldehyde in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NVZ
- Type
- protein
- Length
- 2,438 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xanthine DEHYDROGENASE/OXIDASE
- EC
- 1.17.1.4, 1.17.3.2
- UniProt
- P80457
- Ligands
- FES, FAD, MTE, MOS, I3A
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, J | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 164 | 32% helix, 19% strand | P80457 |
| B, K | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 305 | 36% helix, 24% strand | P80457 |
| C | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 755 | 33% helix, 25% strand | P80457 |
| L | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 745 | 33% helix, 26% strand | P80457 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, C, J, L
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, J, K
- MTE · Phosphonic acidmono-(2-amino-5,6-dimercapto-4-oxo-3,7,8A,9,10,10A-hexahydro-4H-8-oxa-1,3,9,10-tetraaza-anthracen-7-ylmethyl)ester · ligand · 2 copies · chains A, C, J, L
- MOS · Dioxothiomolybdenum(vi) ion · ligand · 2 copies · chains C, L
- I3A · 1H-indole-3-carbaldehyde · ligand · 2 copies · chains C, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.87 | 0.88 | 93 | FAD |
| 2 | 1184 | 0.86 | 0.87 | 106 | FAD |
| 3 | 571 | 0.83 | 0.89 | 72 | empty |
| 4 | 586 | 0.79 | 0.85 | 66 | empty |
| 5 | 760 | 0.79 | 0.83 | 93 | empty |
Interfaces
9 interfaces between chains.
- C–L · 3017 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 2130 Ų buried · 35 hydrogen bonds · protein-protein
- J–L · 2119 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1452 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1407 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3NVZ · Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3-Aldehyde · the same entry in another collection · chain A against A, TM-score 1.00
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 P80457
- Elsewhere: RCSB PDB 3NVZ · PDBe 3NVZ · UniProt P80457
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