5MS3 | pdb_00005ms3

Kallikrein-related peptidase 8 calcium complex

• PDB DOI: https://doi.org/10.2210/pdb5MS3/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-30 Released: 2018-01-17 
• Deposition Author(s): Debela, M., Magdolen, V., Skala, W., Bode, W., Brandstetter, H., Goettig, P.
• Funding Organization(s): Austrian Science Fund

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Specificity profiles and antagonistic Ca2+ and Zn2+ regulation of human KLK8/neuropsin activity by modules identified in crystal structures

Debela, M., Magdolen, V., Skala, W., Craik, C.S., Schneider, E.L., Biniossek, M.L., Schilling, O., Elsaesser, B., Bode, W., Brandstetter, H., Goettig, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.52 kDa 
• Atom Count: 1,796 
• Modeled Residue Count: 228 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kallikrein-8	A	228	Homo sapiens	Mutation(s): 0  Gene Names: KLK8, NRPN, PRSS19, TADG14, UNQ283/PRO322 EC: 3.4.21.118
UniProt & NIH Common Fund Data Resources
Find proteins for O60259 (Homo sapiens) Explore O60259  Go to UniProtKB:  O60259
PHAROS:  O60259 GTEx:  ENSG00000129455

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.997	α = 90
b = 51.741	β = 90
c = 82.863	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Debela, M., Magdolen, V., Skala, W., Bode, W., Brandstetter, H., Goettig, P.

---

Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P25003-B21

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary