Research workbench

Crystal structure of human granzyme H with an inhibitor

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

PDB: 3TJU
Type: protein
Length: 229 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Granzyme H; Ac-ptsy-cmk inhibitor
EC: 3.4.21.-
UniProt: P20718
Ligands: ACE, SO4, 0QE
Pockets: 1 · best druggability 0.40

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Granzyme H (EC 3.4.21.-)	protein	225	10% helix, 40% strand	P20718
B	Ac-ptsy-cmk inhibitor	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A
0QE · Chloromethane · ion · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	129	0.40	0.75	21	SO4

Interfaces

1 interface between chains.

A–B · 412 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, nonstandard).

Compared structures

3TJU · Crystal structure of human granzyme H with an inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P20718 · AlphaFold monomer V2.0 prediction for granzyme H (P20718) · 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 P20718
Elsewhere: RCSB PDB 3TJU · PDBe 3TJU · UniProt P20718

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.