6A8O

Crystal structures of the serine protease domain of murine plasma kallikrein with peptide inhibitor mupain-1-16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.217 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of plasma kallikrein reveals the unusual flexibility of the S1 pocket triggered by Glu217.

Xu, M.Chen, Y.Xu, P.Andreasen, P.A.Jiang, L.Li, J.Huang, M.

(2018) FEBS Lett 592: 2658-2667

  • DOI: 10.1002/1873-3468.13191
  • Primary Citation of Related Structures:  
    6A8O

  • PubMed Abstract: 
  • Serine proteases play important roles in numerous physiological and pathophysiological processes. Moreover, serine proteases are classical subjects for studies of catalytic and inhibitory mechanisms of enzymes. Here, we determined the crystal structures of a serine protease, murine plasma kallikrein (mPK), and its complex with a peptidic inhibitor ...

    Serine proteases play important roles in numerous physiological and pathophysiological processes. Moreover, serine proteases are classical subjects for studies of catalytic and inhibitory mechanisms of enzymes. Here, we determined the crystal structures of a serine protease, murine plasma kallikrein (mPK), and its complex with a peptidic inhibitor. Although mPK in the complex adopts a canonical protease structure, the apo-mPK exhibits a previously unobserved structural feature: the entrance of the intact S1 pocket is blocked by Glu217. In addition, molecular dynamics simulations and functional assays support the flexibility of Glu217 and suggest that this flexibility plays a role in regulating the activity of serine proteases.


    Organizational Affiliation

    Fujian Institute of Research on the Structure of Matter, State Key Laboratory of Structural Chemistry, Chinese Academy of Sciences, Fuzhou, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Plasma kallikreinA, B248Mus musculusMutation(s): 1 
Gene Names: Klkb1Klk3Pk
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26262
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
peptide inhibitor,C [auth P]10SynthemiopsisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
MRZ
Query on MRZ

Download Ideal Coordinates CCD File 
F [auth P]piperidine-1-carboximidamide
C6 H13 N3
QUUYRYYUKNNNNS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.26α = 90
b = 82.45β = 90
c = 105.32γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31370737, 31400637, 31170707, 31570745, 31670739, 21603033, U1405229

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary