MolNFT v1 · #64525 · protein
Crystal structure of blue copper oxidase from nitrosomonas europaea
3G5W · Multicopper oxidase type 1: “Crystal structure of blue copper oxidase from nitrosomonas europaea”. X-ray diffraction, 3 ligands (C1O, C2O, CU), 20 pockets (best druggability 0.89). MolNFT v1 #64525 on GenesisL1: 3D structure…
- PDB
- 3G5W
- Type
- protein
- Length
- 1,908 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multicopper oxidase type 1
- UniProt
- Q82VX3
- Ligands
- C1O, C2O, CU
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Multicopper oxidase type 1 | protein | 318 | 7% helix, 45% strand | Q82VX3 |
Ligands and binding sites
- C1O · Cu-O linkage · ligand · 6 copies · chains A, C, B, D, E, F
- C2O · Cu-O-Cu linkage · ligand · 6 copies · chains A, B, C, D, E, F
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.89 | 0.91 | 85 | GOL |
| 2 | 958 | 0.83 | 0.85 | 64 | empty |
| 3 | 950 | 0.83 | 0.84 | 66 | empty |
| 4 | 327 | 0.69 | 0.82 | 43 | empty |
| 5 | 319 | 0.68 | 0.82 | 38 | empty |
Interfaces
12 interfaces between chains.
- D–F · 1695 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1694 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1692 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1690 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1689 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3G5W · Crystal structure of Blue Copper Oxidase from Nitrosomonas europaea · 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 Q82VX3
- Elsewhere: RCSB PDB 3G5W · PDBe 3G5W · UniProt Q82VX3
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