1NL1 | pdb_00001nl1

BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM ION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.253 (Depositor) 
  • R-Value Work: 
    0.219 (Depositor) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history

Literature

Structural basis of membrane binding by Gla domains of vitamin K-dependent proteins.

Huang, M.Rigby, A.C.Morelli, X.Grant, M.A.Huang, G.Furie, B.Seaton, B.Furie, B.C.

(2003) Nat Struct Biol 10: 751-756

  • DOI: https://doi.org/10.1038/nsb971
  • Primary Citation Related Structures: 
    1NL1, 1NL2

  • PubMed Abstract: 

    In a calcium-dependent interaction critical for blood coagulation, vitamin K-dependent blood coagulation proteins bind cell membranes containing phosphatidylserine via gamma-carboxyglutamic acid-rich (Gla) domains. Gla domain-mediated protein-membrane interaction is required for generation of thrombin, the terminal enzyme in the coagulation cascade, on a physiologic time scale. We determined by X-ray crystallography and NMR spectroscopy the lysophosphatidylserine-binding site in the bovine prothrombin Gla domain. The serine head group binds Gla domain-bound calcium ions and Gla residues 17 and 21, fixed elements of the Gla domain fold, predicting the structural basis for phosphatidylserine specificity among Gla domains. Gla domains provide a unique mechanism for protein-phospholipid membrane interaction. Increasingly Gla domains are being identified in proteins unrelated to blood coagulation. Thus, this membrane-binding mechanism may be important in other physiologic processes.


  • Organizational Affiliation
    • Center for Hemostasis and Thrombosis Research, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, 330 Brookline Avenue, Boston, Massachusetts 02215, USA.

Macromolecule Content 

  • Total Structure Weight: 17.9 kDa 
  • Atom Count: 1,424 
  • Modeled Residue Count: 147 
  • Deposited Residue Count: 147 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Prothrombin147Bos taurusMutation(s): 10 
EC: 3.4.21.5
UniProt
Find proteins for P00735 (Bos taurus)
Explore P00735 
Go to UniProtKB:  P00735
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00735
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.253 (Depositor) 
  • R-Value Work:  0.219 (Depositor) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.188α = 90
b = 53.443β = 90
c = 128.173γ = 90
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-08-16
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2023-11-15
    Changes: Data collection