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Crystal structure of yeast SCO1

Analyse Crystal structure of yeast SCO1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2B7K
Type: protein
Length: 638 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SCO1 protein
UniProt: P23833
Ligands: PT
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	SCO1 protein	protein	155	35% helix, 21% strand	P23833
B, D	SCO1 protein	protein	164	34% helix, 20% strand	P23833

Ligands and binding sites

PT · Platinum (II) ion · metal · 2 copies · chains B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1071	0.83	0.84	88	empty
2	81	0.73	0.96	20	PT
3	80	0.72	0.96	23	PT
4	102	0.37	0.75	21	empty
5	103	0.34	0.73	17	empty

Interfaces

5 interfaces between chains.

B–C · 945 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 933 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 277 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 276 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 120 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2B7K · Crystal Structure of Yeast Sco1 · the same entry in another collection · chain A against A, TM-score 1.00
P23833 · AlphaFold monomer V2.0 prediction for protein SCO1, mitochondrial (P23833) · a predicted model of the same protein · chain B 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 P23833
Elsewhere: RCSB PDB 2B7K · PDBe 2B7K · UniProt P23833

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