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Crystal structure of active human granzyme M

Analyse Crystal structure of active human granzyme M in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZGC
Type: protein
Length: 231 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Granzyme M
EC: 3.4.21.-
UniProt: P51124
Ligands: SO4
Pockets: 3 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Granzyme M (EC 3.4.21.-)	protein	231	10% helix, 35% strand	P51124

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	96	0.44	0.79	17	empty
2	87	0.41	0.78	19	empty
3	75	0.36	0.76	17	empty

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2ZGC · Crystal Structure of Active Human Granzyme M · the same entry in another collection · chain A against A, TM-score 1.00
P51124 · AlphaFold monomer V2.0 prediction for granzyme M (P51124) · 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 P51124
Elsewhere: RCSB PDB 2ZGC · PDBe 2ZGC · UniProt P51124

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