MolNFT v1 · #9946 · protein
Red copper protein nitrosocyanin from nitrosomonas europaea
1IBY: “Red copper protein nitrosocyanin from nitrosomonas europaea”. X-ray diffraction, 1 ligand (CU), 9 pockets (best druggability 0.71). MolNFT v1 #9946 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1IBY
- Type
- protein
- Length
- 448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrosocyanin
- UniProt
- Q820S6
- Ligands
- CU
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 66% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Nitrosocyanin | protein | 112 | 3% helix, 66% strand | Q820S6 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
- HEZ · Hexane-1,6-diol · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.71 | 0.96 | 25 | empty |
| 2 | 80 | 0.55 | 0.85 | 19 | HEZ |
| 3 | 74 | 0.52 | 0.84 | 18 | HEZ |
| 4 | 101 | 0.48 | 0.81 | 16 | empty |
| 5 | 72 | 0.39 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1073 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 982 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 942 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1IBY · Red copper protein nitrosocyanin 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 Q820S6
- Elsewhere: RCSB PDB 1IBY · PDBe 1IBY · UniProt Q820S6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.