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Manganese peroxidase-SM(III) complex

Analyse Manganese peroxidase-SM(III) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YZR
Type: protein
Length: 357 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxidase manganese-dependent I
EC: 1.11.1.13
UniProt: Q02567
Ligands: HEM, NAG, MAN, CA, SM
Pockets: 3 · best druggability 0.81

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxidase manganese-dependent I (EC 1.11.1.13)	protein	357	39% helix, 6% strand	Q02567

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
MAN · alpha-D-mannopyranose · sugar · chains A
CA · Calcium ion · metal · 2 copies · chains A
SM · Samarium (III) ion · metal · chains A
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

3 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	394	0.81	0.89	47	SM, HEM
2	224	0.52	0.77	37	empty
3	108	0.43	0.78	25	GOL

Modifications

Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation, O-glycosylation).

Compared structures

1YZR · Manganese peroxidase-Sm(III) complex · the same entry in another collection · chain A against A, TM-score 1.00
Q02567 · AlphaFold monomer V2.0 prediction for manganese peroxidase 1 (Q02567) · a predicted model of the same protein · chain A 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 Q02567
Elsewhere: RCSB PDB 1YZR · PDBe 1YZR · UniProt Q02567

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