Research workbench

MOUSE SOD1

Analyse MOUSE SOD1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GTT
Type: protein
Length: 918 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Superoxide dismutase [cu-zn]
EC: 1.15.1.1
UniProt: P08228
Ligands: ZN
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Superoxide dismutase [cu-zn] (EC 1.15.1.1)	protein	153	6% helix, 41% strand	P08228

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1078	0.78	0.80	99	empty
2	157	0.67	0.88	28	empty
3	174	0.65	0.86	29	empty
4	157	0.64	0.86	34	empty
5	161	0.42	0.73	27	empty

Interfaces

6 interfaces between chains.

A–B · 752 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 750 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 734 Å² buried · 5 hydrogen bonds · protein-protein
A–E · 330 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 294 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3GTT · Mouse SOD1 · the same entry in another collection · chain C against C, TM-score 1.00
P08228 · AlphaFold monomer V2.0 prediction for superoxide dismutase [cu-zn] (P08228) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P08228
Elsewhere: RCSB PDB 3GTT · PDBe 3GTT · UniProt P08228

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