MolNFT v1 · #157639 · protein
Crystal structure of arabidopsis thaliana scoi with copper bound
6N5U · Protein SCO1 homolog 1, mitochondrial: “Crystal structure of arabidopsis thaliana scoi with copper bound”. X-ray diffraction, 1 ligand (CU1), 4 pockets (best druggability 0.65). MolNFT v1 #157639 on GenesisL1: 3D structure, binding…
- PDB
- 6N5U
- Type
- protein
- Length
- 479 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein SCO1 homolog 1, mitochondrial
- UniProt
- Q8VYP0
- Ligands
- CU1
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein SCO1 homolog 1, mitochondrial | protein | 161 | 34% helix, 27% strand | Q8VYP0 |
| B | Protein SCO1 homolog 1, mitochondrial | protein | 157 | 36% helix, 27% strand | Q8VYP0 |
Ligands and binding sites
- CU1 · Copper (I) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.65 | 0.78 | 30 | empty |
| 2 | 271 | 0.57 | 0.77 | 29 | empty |
| 3 | 172 | 0.50 | 0.78 | 31 | empty |
| 4 | 52 | 0.23 | 0.72 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–C · 526 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 480 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6N5U · Crystal structure of Arabidopsis thaliana ScoI with copper bound · the same entry in another collection · chain A against A, TM-score 1.00
- Q8VYP0 · AlphaFold monomer V2.0 prediction for protein SCO1 homolog 1, mitochondrial (Q8VYP0) · a predicted model of the same protein · chain B 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 Q8VYP0
- Elsewhere: RCSB PDB 6N5U · PDBe 6N5U · UniProt Q8VYP0
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