4EB1

Hyperstable in-frame insertion variant of antithrombin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Type II antithrombin deficiency caused by a large in-frame insertion: structural, functional and pathological relevance.

Martinez-Martinez, I.Johnson, D.J.Yamasaki, M.Navarro-Fernandez, J.Ordonez, A.Vicente, V.Huntington, J.A.Corral, J.

(2012) J Thromb Haemost 10: 1859-1866

  • DOI: 10.1111/j.1538-7836.2012.04839.x
  • Primary Citation of Related Structures:  
    4EB1

  • PubMed Abstract: 
  • The metastable native conformation of serpins is required for their protease inhibition mechanism, but also renders them vulnerable to missense mutations that promote protein misfolding with pathological consequences.


    Organizational Affiliation

    Centro Regional de Hemodonación, University of Murcia, Regional Campus of International Excellence Campus Mare Nostrum, Murcia, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antithrombin-IIIA [auth I]440Homo sapiensMutation(s): 1 
Gene Names: SERPINC1AT3PRO0309
Find proteins for P01008 (Homo sapiens)
Explore P01008 
Go to UniProtKB:  P01008
NIH Common Fund Data Resources
PHAROS:  P01008
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antithrombin-IIIB [auth L]432Homo sapiensMutation(s): 0 
Gene Names: SERPINC1AT3PRO0309
Find proteins for P01008 (Homo sapiens)
Explore P01008 
Go to UniProtKB:  P01008
NIH Common Fund Data Resources
PHAROS:  P01008
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth A], D [auth B]2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth I], F [auth I]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.75α = 90
b = 101.75β = 105.42
c = 88.81γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-09-19
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Refinement description, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary