MolNFT v1 · #9908 · protein

Human granzyme B in complex with ac-iepd-cho

1IAU: “Human granzyme B in complex with ac-iepd-cho”. X-ray diffraction, 6 ligands (ACE, NAG, MAN), 1 pocket (best druggability 0.34). MolNFT v1 #9908 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1IAU
Type: protein
Length: 230 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Granzyme B; Acetyl-isoleucyl-glutamyl-prolyl-aspartyl-aldehyde peptide inhibitor
EC: 3.4.21.79
UniProt: P10144
Ligands: ACE, NAG, MAN, BMA, FUC, ZN
Pockets: 1 · best druggability 0.34

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Granzyme B (EC 3.4.21.79)	protein	226	10% helix, 38% strand	P10144
B	Acetyl-isoleucyl-glutamyl-prolyl-aspartyl-aldehyde peptide inhibitor	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
MAN · alpha-D-mannopyranose · sugar
BMA · beta-D-mannopyranose · sugar
FUC · alpha-L-fucopyranose · sugar · chains A
ZN · Zinc ion · metal · 5 copies · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	74	0.34	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 471 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 2 glycan, 1 covalent, 1 modified (disulfide, N-glycosylation, covalent ligand, nonstandard).

Compared structures

1IAU · Human granzyme B in complex with ac-iepd-cho · the same entry in another collection · chain A against A, TM-score 1.00
P10144 · AlphaFold monomer V2.0 prediction for granzyme B (P10144) · 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 P10144
Elsewhere: RCSB PDB 1IAU · PDBe 1IAU · UniProt P10144

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