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Crystal structure of human Cu-Zn Superoxide Dismutase 1 in complex with 1,2,10-Decanetriol

Analyse Crystal structure of human Cu-Zn Superoxide Dismutase 1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8YD3
Type: protein
Length: 1,518 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.96
Source: Homo sapiens
Molecule: Superoxide dismutase [Cu-Zn]
EC: 1.15.1.1
UniProt: P00441
Ligands: A1LYN, ZN
Pockets: 14 · best druggability 0.77

Structure

x-ray diffraction · resolution 1.96 · 3 distinct chains · 6% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, I, J	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	protein	154	6% helix, 39% strand	P00441
G	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	protein	133	4% helix, 47% strand	P00441
H	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	protein	153	7% helix, 39% strand	P00441

Ligands and binding sites

A1LYN · (2S)-decane-1,2,10-triol · ligand · 9 copies · chains A, B, D, C, F, H, I, J
ZN · Zinc ion · metal · 9 copies · chains A, B, C, D, E, F, H, I, J
GOL · Glycerol · additive · 5 copies · chains A, B, C, D, F

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

Pockets

14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1133	0.77	0.79	114	empty
2	328	0.66	0.81	51	empty
3	174	0.65	0.86	29	empty
4	167	0.64	0.85	33	empty
5	379	0.62	0.78	43	empty

Interfaces

13 interfaces between chains.

C–D · 761 Å² buried · 4 hydrogen bonds · protein-protein
I–J · 728 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 727 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 726 Å² buried · 5 hydrogen bonds · protein-protein
G–H · 719 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

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 P00441
Elsewhere: RCSB PDB 8YD3 · PDBe 8YD3 · UniProt P00441

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