1M1J | pdb_00001m1j

Crystal structure of native chicken fibrinogen with two different bound ligands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.256 (Depositor) 
  • R-Value Work: 
    0.227 (Depositor) 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history

Literature

Crystal Structure of Native Chicken Fibrinogen at 2.7 A Resolution

Yang, Z.Kollman, J.M.Pandi, L.Doolittle, R.F.

(2001) Biochemistry 40: 12515-12523

  • DOI: https://doi.org/10.1021/bi011394p
  • Primary Citation Related Structures: 
    1M1J

  • PubMed Abstract: 

    The crystal structure of native chicken fibrinogen (320 kDa) complexed with two synthetic peptides has been determined at a resolution of 2.7 A. The structure provides the first atomic-resolution view of the polypeptide chain arrangement in the central domain where the two halves of the molecule are joined, as well as of a putative thrombin-binding site. The amino-terminal segments of the alpha and beta chains, including fibrinopeptides A and B, are not visible in electron density maps, however, and must be highly disordered. The alphaC domain is also very disordered. A residue by residue analysis of the coiled coils with regard to temperature factor shows a strong correlation between mobility and plasmin attack sites. It is concluded that structural flexibility is an inherent feature of fibrinogen that plays a key role in both its conversion to fibrin and its subsequent destruction by plasmin.


  • Organizational Affiliation
    • Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093-0634, USA.

Macromolecule Content 

  • Total Structure Weight: 311.78 kDa 
  • Atom Count: 16,117 
  • Modeled Residue Count: 1,984 
  • Deposited Residue Count: 2,744 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fibrinogen alpha subunit
A, D
491Gallus gallusMutation(s): 0 
UniProt
Find proteins for P14448 (Gallus gallus)
Explore P14448 
Go to UniProtKB:  P14448
Entity Groups
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UniProt GroupP14448
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fibrinogen beta chain
B, E
464Gallus gallusMutation(s): 0 
UniProt
Find proteins for Q02020 (Gallus gallus)
Explore Q02020 
Go to UniProtKB:  Q02020
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UniProt GroupQ02020
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fibrinogen gamma chain
C, F
409Gallus gallusMutation(s): 0 
UniProt
Find proteins for O93568 (Gallus gallus)
Explore O93568 
Go to UniProtKB:  O93568
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UniProt GroupO93568
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
GLY-PRO-ARG-PRO peptide
G, H
4N/AMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
GLY-HIS-ARG-PRO peptide
I, J
4N/AMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDG

Query on NDG



Download:Ideal Coordinates CCD File
K [auth B],
M [auth C],
P [auth E],
R [auth F],
V [auth J]
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
N [auth C],
S [auth F],
U [auth I]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
L [auth B],
O [auth C],
Q [auth E],
T [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.256 (Depositor) 
  • R-Value Work:  0.227 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.09α = 90
b = 100.02β = 105.79
c = 200.09γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-26
    Type: Initial release
  • Version 1.1: 2008-04-28
    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, Derived calculations, Structure summary
  • Version 2.1: 2024-10-30
    Changes: Data collection, Database references, Refinement description, Structure summary