1N86

Crystal structure of human D-dimer from cross-linked fibrin complexed with GPR and GHRPLDK peptide ligands.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface.

Yang, Z.Pandi, L.Doolittle, R.F.

(2002) Biochemistry 41: 15610-15617

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of fragment double-D from factor XIII-cross-linked lamprey fibrin has been determined at 2.9 A resolution. The 180 kDa covalent dimer was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens, but not ...

    The crystal structure of fragment double-D from factor XIII-cross-linked lamprey fibrin has been determined at 2.9 A resolution. The 180 kDa covalent dimer was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens, but not that of lamprey, corresponds to the B-knob exposed by thrombin. The structure was determined by molecular replacement, a recently determined structure of lamprey fragment D being used as a search model. GHRPam was found in both the gamma- and beta-chain holes. Unlike the situation with fragment D, the crystal packing of the cross-linked double-D structure exhibits two different D-D interfaces, each gamma-chain facing gamma-chains on two other molecules. One of these (interface I) involves the asymmetric interface observed in all other D fragments and related structures. The other (interface II) encompasses a completely different set of residues. The two abutments differ in that interface I results in an "in line" arrangement of abutting molecules and the interface II in a "zigzag" arrangement. So far as can be determined (the electron density could only be traced on one side of the cross-links), it is the gamma-chains of the newly observed zigzag units (interface II) that are joined by the reciprocal epsilon-amino-gamma-glutamyl cross-links. Auspiciously, the same novel D-D interface was observed in two lower-resolution crystal structures of human double-D preparations that had been crystallized under unusual circumstances. These observations show that double-D structures are linked in a way that is sufficiently flexible to accommodate different D-D interfaces under different circumstances.


    Related Citations: 
    • Crystal structure of fragment double-D from human fibrin with two different bound ligands.
      Everse, S.J.,Spraggon, G.,Veerapandian, L.,Riley, M.,Doolittle, R.F.
      (1998) Biochemistry 37: 8637
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fibrin alpha/alpha-E chain
A, D
87Homo sapiensMutation(s): 0 
Gene Names: FGA
Find proteins for P02671 (Homo sapiens)
Go to Gene View: FGA
Go to UniProtKB:  P02671
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fibrin beta chain
B, E
328Homo sapiensMutation(s): 0 
Gene Names: FGB
Find proteins for P02675 (Homo sapiens)
Go to Gene View: FGB
Go to UniProtKB:  P02675
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fibrin gamma chain
C, F
324Homo sapiensMutation(s): 0 
Gene Names: FGG
Find proteins for P02679 (Homo sapiens)
Go to Gene View: FGG
Go to UniProtKB:  P02679
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
fibrin alpha chain peptide ligand fragment Gly-Pro-Arg
G, H
3Homo sapiensMutation(s): 0 
Gene Names: FGA
Find proteins for P02671 (Homo sapiens)
Go to Gene View: FGA
Go to UniProtKB:  P02671
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
fibrin beta chain peptide ligand fragment Gly-His-Arg-Pro-Leu-Asp-Lys
I, J
7Homo sapiensMutation(s): 0 
Gene Names: FGB
Find proteins for P02675 (Homo sapiens)
Go to Gene View: FGB
Go to UniProtKB:  P02675
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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B, C, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NDG
Query on NDG

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Download CCD File 
B, E, I, J
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.328α = 90.00
b = 130.093β = 90.00
c = 298.313γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-07
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance