5GVT | pdb_00005gvt

Crystal structures of the serine protease domain of murine plasma kallikrein

• PDB DOI: https://doi.org/10.2210/pdb5GVT/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2016-09-06 Released: 2017-11-22 
• Deposition Author(s): Xu, M., Jiang, L., Huang, M.
• Funding Organization(s): the Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.253 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of the Serine Protease Domain of Murine Plasma Kallikrein

Xu, M., Xu, P., Zhou, X., Andreasen, P., Jiang, L., Huang, M.

(2017) Chin J Struct Chem 36: 242-249

• DOI: https://doi.org/10.14102/j.cnki.0254-5861.2011-1305

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.44 kDa 
• Atom Count: 3,680 
• Modeled Residue Count: 461 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasma kallikrein	A, B	250	Mus musculus	Mutation(s): 1  Gene Names: Klkb1, Klk3, Pk EC: 3.4.21.34
UniProt & NIH Common Fund Data Resources
Find proteins for P26262 (Mus musculus) Explore P26262  Go to UniProtKB:  P26262
IMPC:  MGI:102849

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMA	C [auth A], D [auth A]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
MAN	E [auth B], F [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.253 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.231	α = 90
b = 85.556	β = 90
c = 109.229	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-22 
Deposition Author(s): Xu, M., Jiang, L., Huang, M.

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Funding Organization	Location	Grant Number
the Natural Science Foundation of China	China	31570745, 31370737, 31400637

Revision History  

• Version 1.0: 2017-11-22
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2025-09-17
  Changes: Advisory, Derived calculations, Structure summary