Research workbench

Sod-3 azide complex

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

PDB: 5AG2
Type: protein
Length: 389 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Superoxide dismutase [mn] 2, mitochondrial
EC: 1.15.1.1
UniProt: P41977
Ligands: MN, AZI, SO4
Pockets: 1 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Superoxide dismutase [mn] 2, mitochondrial (EC 1.15.1.1)	protein	194	57% helix, 13% strand	P41977
C	Superoxide dismutase [mn] 2, mitochondrial (EC 1.15.1.1)	protein	195	56% helix, 13% strand	P41977

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains A, C
AZI · Azide ion · ion · 2 copies · chains A, C
SO4 · Sulfate ion · ion · chains C
ACT · Acetate ion · additive · chains A
MLI · Malonate ion · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	154	0.59	0.83	28	empty

Interfaces

1 interface between chains.

A–C · 826 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (oxidation).

Compared structures

5AG2 · SOD-3 azide complex · the same entry in another collection · chain A against A, TM-score 1.00
P41977 · AlphaFold monomer V2.0 prediction for superoxide dismutase [mn] 2, mitochondrial (P41977) · a predicted model of the same protein · chain C against A, TM-score 1.00

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 P41977
Elsewhere: RCSB PDB 5AG2 · PDBe 5AG2 · UniProt P41977

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