MolNFT v1 · #23045 · protein

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

1TO5 · Superoxide dismutase: “Structure of the cytosolic CU,ZN sod from S. mansoni”. X-ray diffraction, 2 ligands (ZN, CU), 5 pockets (best druggability 0.73). MolNFT v1 #23045 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1TO5
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: ZN, CU
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Superoxide dismutase (EC 1.15.1.1)	protein	156	2% helix, 39% strand	Q01137

Ligands and binding sites

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

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1197	0.73	0.77	108	empty
2	168	0.51	0.79	34	empty
3	177	0.47	0.76	24	empty
4	60	0.32	0.76	16	empty
5	50	0.26	0.74	15	empty

Interfaces

5 interfaces between chains.

A–B · 677 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 670 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 240 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 124 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 89 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1TO5 · 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 1TO5 · PDBe 1TO5 · UniProt Q01137

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