1LWU

Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide.

Yang, Z.Spraggon, G.Pandi, L.Everse, S.J.Riley, M.Doolittle, R.F.

(2002) Biochemistry 41: 10218-10224


  • PubMed Abstract: 
  • The crystal structure of fragment D from lamprey fibrinogen has been determined at 2.8 A resolution. The 89 kDa protein was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens-but not lamprey-corresponds to the B knob exp ...

    The crystal structure of fragment D from lamprey fibrinogen has been determined at 2.8 A resolution. The 89 kDa protein was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens-but not lamprey-corresponds to the B knob exposed by thrombin. Because lamprey fragment D is more than 50% identical in sequence with human fragment D, the structure of which has been reported previously, it was possible to use the method of molecular replacement. The space group of the lamprey crystals is P1; there are four molecules in the unit cell. Although the fragments are packed head to head by the same D:D interface as is observed in other related preparations containing fragments D, the tails are uniquely joined by an unnatural association of the terminal sections of the residual coiled coils from adjacent molecules. Some features of the lamprey structure are clearer than have been observed in previous fragment D structures, including the beta-chain carbohydrate cluster, for one, and the important gamma-chain carboxyl-terminal segment, for another. The most significant differences between the lamprey and human structures occur in connecting loops at the entryways to the beta-chain and gamma-chain binding pockets.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen alpha-1 chain
A, D, G, J
119Petromyzon marinusN/A
Find proteins for P02674 (Petromyzon marinus)
Go to UniProtKB:  P02674
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen beta chain
B, E, H, K
323Petromyzon marinusN/A
Find proteins for P02678 (Petromyzon marinus)
Go to UniProtKB:  P02678
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen gamma chain
C, F, I, L
323Petromyzon marinusGene Names: FGG
Find proteins for P04115 (Petromyzon marinus)
Go to Gene View: FGG
Go to UniProtKB:  P04115
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ligand Gly-His-Arg-Pro-NH2
M, N, O, P
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NH2
Query on NH2

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Download CCD File 
M, N, O, P
AMINO GROUP
H2 N
QGZKDVFQNNGYKY-UHFFFAOYAF
 Ligand Interaction
CA
Query on CA

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Download CCD File 
B, C, E, F, H, I, K, L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
B, C, F, H, J, L, N, P
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
GAL
Query on GAL

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H
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
E, H
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NDG
Query on NDG

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Download CCD File 
B, D, H, K, M, N, O
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
C, E, F, H, I, L
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
M, N, O, P
NON-POLYMERH2 N

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.245 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 76.735α = 88.81
b = 47.654β = 97.23
c = 244.650γ = 86.17
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-23
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance