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Crystal structure of kallikrein-related peptidase 4

Analyse Crystal structure of kallikrein-related peptidase 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KGA
Type: protein
Length: 442 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kallikrein-4
EC: 3.4.21.-
UniProt: Q9Y5K2
Ligands: NI
Pockets: 5 · best druggability 0.63

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kallikrein-4 (EC 3.4.21.-)	protein	221	10% helix, 35% strand	Q9Y5K2
B	Kallikrein-4 (EC 3.4.21.-)	protein	221	10% helix, 34% strand	Q9Y5K2

Ligands and binding sites

NI · Nickel (II) ion · metal · 4 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	458	0.63	0.77	35	EDO
2	52	0.43	0.83	16	empty
3	50	0.33	0.78	16	empty
4	66	0.33	0.76	17	empty
5	53	0.27	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 253 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

4KGA · Crystal structure of kallikrein-related peptidase 4 · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y5K2 · AlphaFold monomer V2.0 prediction for kallikrein-4 (Q9Y5K2) · 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 Q9Y5K2
Elsewhere: RCSB PDB 4KGA · PDBe 4KGA · UniProt Q9Y5K2

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