3LMS

Structure of human activated thrombin-activatable fibrinolysis inhibitor, TAFIa, in complex with tick-derived funnelin inhibitor, TCI.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Insights into the molecular inactivation mechanism of human activated thrombin-activatable fibrinolysis inhibitor

Sanglas, L., Arolas, J.L., Valnickova, Z., Aviles, F.X., Enghild, J.J., Gomis-Ruth, F.X.

(2010) J Thromb Haemost 8: 1056-1065

  • DOI: https://doi.org/10.1111/j.1538-7836.2010.03740.x
  • Primary Citation of Related Structures:  
    3LMS

  • PubMed Abstract: 

    Thrombin-activatable fibrinolysis inhibitor (TAFI) is a validated target for thrombotic diseases. TAFI is converted in vivo to activated TAFI (TAFIa) by removal of its pro-domain. Whereas TAFI is stable and persists in the circulation, possibly in complex with plasminogen, TAFIa is unstable and poorly soluble, with a half-life of minutes.

    • Organizational Affiliation: 

    Departament de Bioquímica i Biologia Molecular, Facultat de Ciències, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxypeptidase B2309Homo sapiensMutation(s): 0 
EC: 3.4.17.20
UniProt & NIH Common Fund Data Resources
Find proteins for Q96IY4 (Homo sapiens)
Explore Q96IY4 
Go to UniProtKB:  Q96IY4
PHAROS:  Q96IY4
GTEx:  ENSG00000080618 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96IY4
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxypeptidase inhibitor74Rhipicephalus bursaMutation(s): 0 
UniProt
Find proteins for Q5EPH2 (Rhipicephalus bursa)
Explore Q5EPH2 
Go to UniProtKB:  Q5EPH2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5EPH2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
M [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
GLY
Query on GLY
Download Ideal Coordinates CCD File 
D [auth A]GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA
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J [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K
Download Ideal Coordinates CCD File 
K [auth A],
L [auth A]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
N [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.18α = 90
b = 157.18β = 90
c = 57.07γ = 120
Software Package:
Software NamePurpose
ProDCdata collection
AMoREphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description