MolNFT v1 · #9948 · protein
Red copper protein nitrosocyanin from nitrosomonas europaea
1IC0: “Red copper protein nitrosocyanin from nitrosomonas europaea”. X-ray diffraction, 1 ligand (CU), 17 pockets (best druggability 0.75). MolNFT v1 #9948 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1IC0
- Type
- protein
- Length
- 664 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrosocyanin
- UniProt
- Q820S6
- Ligands
- CU
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 66% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrosocyanin | protein | 110 | 3% helix, 64% strand | Q820S6 |
| B, C, D, E | Nitrosocyanin | protein | 111 | 3% helix, 67% strand | Q820S6 |
| F | Nitrosocyanin | protein | 110 | 3% helix, 67% strand | Q820S6 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.75 | 0.96 | 25 | empty |
| 2 | 858 | 0.74 | 0.78 | 89 | empty |
| 3 | 94 | 0.74 | 0.96 | 26 | empty |
| 4 | 61 | 0.49 | 0.84 | 14 | empty |
| 5 | 57 | 0.46 | 0.83 | 12 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1008 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 956 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 948 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 939 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 865 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1IC0 · Red copper protein nitrosocyanin from nitrosomonas europaea · the same entry in another collection · chain C against C, 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 1IC0 · PDBe 1IC0 · UniProt Q820S6
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