MolNFT v1 · #32009 · protein

Human kallikrein 4 complex with zinc and P-aminobenzamidine

2BDH · Kallikrein-4: “Human kallikrein 4 complex with zinc and P-aminobenzamidine”. X-ray diffraction, 2 ligands (PBZ, ZN), 8 pockets (best druggability 0.76). MolNFT v1 #32009 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2BDH
Type: protein
Length: 892 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kallikrein-4
EC: 3.4.21.-
UniProt: Q9Y5K2
Ligands: PBZ, ZN
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Kallikrein-4 (EC 3.4.21.-)	protein	223	9% helix, 34% strand	Q9Y5K2

Ligands and binding sites

PBZ · P-amino benzamidine · ligand · 4 copies · chains A, D, B, C
ZN · Zinc ion · metal · chains A

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	934	0.76	0.79	124	PBZ
2	370	0.64	0.79	60	PBZ
3	147	0.50	0.79	27	empty
4	159	0.47	0.77	26	empty
5	125	0.43	0.76	27	empty

Interfaces

4 interfaces between chains.

B–C · 529 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 482 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 471 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 463 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

2BDH · Human Kallikrein 4 complex with zinc and p-aminobenzamidine · 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 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 Q9Y5K2
Elsewhere: RCSB PDB 2BDH · PDBe 2BDH · UniProt Q9Y5K2

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