5F8Z | pdb_00005f8z

The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor pkalin-1

• PDB DOI: https://doi.org/10.2210/pdb5F8Z/pdb
• Entry: 5F8Z supersedes: 4ZJ4

• Classification: HYDROLASE-HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2015-12-09 Released: 2016-12-14 
• Deposition Author(s): Xu, M., Jiang, L., Xu, P., Luo, Z., Andreasen, P., Huang, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.217 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor pkalin-1

Xu, M., Jiang, L., Xu, P., Luo, Z., Andreasen, P., Huang, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.62 kDa 
• Atom Count: 2,207 
• Modeled Residue Count: 249 
• Deposited Residue Count: 249 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasma kallikrein LIGHT CHAIN	A	239	Homo sapiens	Mutation(s): 1  Gene Names: KLKB1, KLK3 EC: 3.4.21.34
UniProt & NIH Common Fund Data Resources
Find proteins for P03952 (Homo sapiens) Explore P03952  Go to UniProtKB:  P03952
PHAROS:  P03952 GTEx:  ENSG00000164344

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYS-PRO-ALA-ARG-PHE-M70-ALA-LEU-PHE-CYS	B	10	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRZ	H [auth B]	piperidine-1-carboximidamide C6 H13 N3 QUUYRYYUKNNNNS-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.217 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.279	α = 90
b = 90.279	β = 90
c = 57.623	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Xu, M., Jiang, L., Xu, P., Luo, Z., Andreasen, P., Huang, M.
• This entry supersedes: 4ZJ4

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2025-09-17
  Changes: Advisory, Derived calculations, Structure summary