MolNFT v1 · #37924 · protein
Crystal structure of human SCO1 complexed with nickel.
2GGT · SCO1 protein homolog, mitochondrial: “Crystal structure of human SCO1 complexed with nickel.”. X-ray diffraction, 2 ligands (NI, CL), 3 pockets (best druggability 0.67). MolNFT v1 #37924 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2GGT
- Type
- protein
- Length
- 327 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SCO1 protein homolog, mitochondrial
- UniProt
- O75880
- Ligands
- NI, CL
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SCO1 protein homolog, mitochondrial | protein | 164 | 34% helix, 29% strand | O75880 |
| B | SCO1 protein homolog, mitochondrial | protein | 163 | 31% helix, 23% strand | O75880 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.67 | 0.82 | 37 | NI, CL |
| 2 | 151 | 0.50 | 0.78 | 22 | empty |
| 3 | 80 | 0.34 | 0.75 | 22 | CL |
Interfaces
1 interface between chains.
- A–B · 659 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2GGT · Crystal structure of human SCO1 complexed with nickel. · the same entry in another collection · chain A against A, TM-score 1.00
- O75880 · AlphaFold monomer V2.0 prediction for protein SCO1 homolog, mitochondrial (O75880) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O75880
- Elsewhere: RCSB PDB 2GGT · PDBe 2GGT · UniProt O75880
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