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: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 2.0 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

  • DOI: 10.1021/bi020299t
  • Primary Citation of Related Structures:  
    1LWU

  • 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 exposed by thrombin ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen alpha-1 chainA, D, G, J119Petromyzon marinusMutation(s): 0 
UniProt
Find proteins for P02674 (Petromyzon marinus)
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Go to UniProtKB:  P02674
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen beta chainB, E, H, K323Petromyzon marinusMutation(s): 0 
UniProt
Find proteins for P02678 (Petromyzon marinus)
Explore P02678 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen gamma chainC, F, I, L323Petromyzon marinusMutation(s): 1 
Gene Names: FGG
UniProt
Find proteins for P04115 (Petromyzon marinus)
Explore P04115 
Go to UniProtKB:  P04115
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Ligand Gly-His-Arg-Pro-NH2M, N, O, P5N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseQ2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
DA [auth F], EA [auth F], MA [auth H], PA [auth I], QA [auth I], U [auth C], V [auth C], Z [auth E]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NDG (Subject of Investigation/LOI)
Query on NDG

Download Ideal Coordinates CCD File 
AB [auth N], DB [auth O], HA [auth H], IA [auth H], R [auth B], TA [auth K], Y [auth D], YA [auth M]2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
GAL (Subject of Investigation/LOI)
Query on GAL

Download Ideal Coordinates CCD File 
NA [auth H]beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
BMA (Subject of Investigation/LOI)
Query on BMA

Download Ideal Coordinates CCD File 
AA [auth E], BA [auth E], KA [auth H]beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN (Subject of Investigation/LOI)
Query on MAN

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BB [auth N] , FA [auth F] , FB [auth P] , JA [auth H] , LA [auth H] , S [auth B] , SA [auth J] , VA [auth L] , 
BB [auth N],  FA [auth F],  FB [auth P],  JA [auth H],  LA [auth H],  S [auth B],  SA [auth J],  VA [auth L],  W [auth C]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth E], GA [auth F], OA [auth H], RA [auth I], T [auth B], UA [auth K], WA [auth L], X [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NH2
Query on NH2

Download Ideal Coordinates CCD File 
CB [auth O], EB [auth P], XA [auth M], ZA [auth N]AMINO GROUP
H2 N
QGZKDVFQNNGYKY-UHFFFAOYAF
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.251 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.735α = 88.81
b = 47.654β = 97.23
c = 244.65γ = 86.17
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: 2002-08-23
    Type: Initial release
  • Version 1.1: 2008-04-01
    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: Advisory, Atomic model, Data collection, Derived calculations, Structure summary