MolNFT v1 · #23044 · protein

Structure of the cytosolic CU,ZN sod from S. mansoni

1TO4 · Superoxide dismutase: “Structure of the cytosolic CU,ZN sod from S. mansoni”. X-ray diffraction, 2 ligands (CU, ZN), 4 pockets (best druggability 0.54). MolNFT v1 #23044 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1TO4
Type: protein
Length: 624 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Superoxide dismutase
EC: 1.15.1.1
UniProt: Q01137
Ligands: CU, ZN
Pockets: 4 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Superoxide dismutase (EC 1.15.1.1)	protein	156	6% helix, 39% strand	Q01137

Ligands and binding sites

CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	198	0.54	0.79	29	empty
2	160	0.50	0.78	30	empty
3	191	0.44	0.74	32	empty
4	127	0.39	0.75	21	empty

Interfaces

2 interfaces between chains.

A–B · 653 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 635 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1TO4 · Structure of the cytosolic Cu,Zn SOD from S. mansoni · the same entry in another collection · chain A against A, TM-score 1.00
Q01137 · AlphaFold monomer V2.0 prediction for superoxide dismutase [cu-zn] (Q01137) · 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 Q01137
Elsewhere: RCSB PDB 1TO4 · PDBe 1TO4 · UniProt Q01137

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