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Crystal structure of human kallikrein 5 in complex with leupeptin and zinc

Analyse Crystal structure of human kallikrein 5 in complex with leupeptin and zinc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PSY
Type: protein
Length: 230 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kallikrein-5; Leupeptin
EC: 3.4.21.-
UniProt: Q9Y337
Ligands: ACE, NAG, ZN
Pockets: 1 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kallikrein-5 (EC 3.4.21.-)	protein	227	10% helix, 34% strand	Q9Y337
B	Leupeptin	protein	3	0% helix, 33% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
ZN · Zinc ion · metal · 3 copies · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	64	0.59	0.90	18	empty

Interfaces

1 interface between chains.

A–B · 385 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 1 covalent, 1 glycan, 1 modified (disulfide, covalent ligand, N-glycosylation, nonstandard).

Compared structures

2PSY · Crystal Structure of Human Kallikrein 5 in complex with Leupeptin and Zinc · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y337 · AlphaFold monomer V2.0 prediction for kallikrein-5 (Q9Y337) · 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 Q9Y337
Elsewhere: RCSB PDB 2PSY · PDBe 2PSY · UniProt Q9Y337

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