MolNFT v1 · #62935 · protein
Crystal structure of desulfo-xanthine oxidase with xanthine
3EUB · Xanthine DEHYDROGENASE/OXIDASE: “Crystal structure of desulfo-xanthine oxidase with xanthine”. X-ray diffraction, 5 ligands (FES, MTE, MOM), 20 pockets (best druggability 0.87). MolNFT v1 #62935 on GenesisL1: 3D structure, binding…
- PDB
- 3EUB
- Type
- protein
- Length
- 4,864 residues
- Chains
- 12
- 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, MTE, MOM, FAD, XAN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 9 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, J | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 162 | 32% helix, 19% strand | P80457 |
| B | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 304 | 35% helix, 23% strand | P80457 |
| C | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 753 | 31% helix, 25% strand | P80457 |
| K | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 302 | 35% helix, 23% strand | P80457 |
| L, U | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 745 | 32% helix, 26% strand | P80457 |
| S | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 161 | 32% helix, 18% strand | P80457 |
| T, 3 | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 305 | 35% helix, 23% strand | P80457 |
| 2 | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 164 | 30% helix, 20% strand | P80457 |
| 4 | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 756 | 32% helix, 25% strand | P80457 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 8 copies · chains A, C, J, L, S, U, 2, 4
- 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 · 4 copies · chains A, C, J, L, S, U, 2, 4
- MOM · Hydroxy(dioxo)molybdenum · ligand · 4 copies · chains C, L, U, 4
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, J, K, S, T, 2, 3
- XAN · Xanthine · ligand · 4 copies · chains U, C, L, 4
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 | 1046 | 0.87 | 0.89 | 100 | FAD |
| 2 | 985 | 0.87 | 0.89 | 94 | FAD |
| 3 | 958 | 0.87 | 0.88 | 95 | FAD |
| 4 | 1111 | 0.86 | 0.87 | 101 | FAD |
| 5 | 964 | 0.83 | 0.85 | 143 | empty |
Interfaces
22 interfaces between chains.
- C–L · 3045 Ų buried · 59 hydrogen bonds · protein-protein
- U–4 · 3041 Ų buried · 59 hydrogen bonds · protein-protein
- A–C · 2142 Ų buried · 39 hydrogen bonds · protein-protein
- J–L · 2129 Ų buried · 35 hydrogen bonds · protein-protein
- 2–4 · 2128 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 3EUB · Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine · the same entry in another collection · chain 4 against 4, 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 3EUB · PDBe 3EUB · UniProt P80457
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