1N73

Fibrin D-Dimer, Lamprey complexed with the PEPTIDE LIGAND: GLY-HIS-ARG-PRO-AMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  1N86, 1N8E

  • 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.


    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-1 chain
A, D
119Petromyzon marinusN/A
Find proteins for P02674 (Petromyzon marinus)
Go to UniProtKB:  P02674
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fibrin beta chain
B, E
323Petromyzon marinusN/A
Find proteins for P02678 (Petromyzon marinus)
Go to UniProtKB:  P02678
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fibrin gamma chain
C, F
330Petromyzon marinusGene Names: FGG
Find proteins for P04115 (Petromyzon marinus)
Go to Gene View: FGG
Go to UniProtKB:  P04115
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
peptide ligand: Gly-his-Arg-Pro-amide
G, H, I, J
4Homo sapiensGene Names: FGB
Find proteins for P02675 (Homo sapiens)
Go to Gene View: FGB
Go to UniProtKB:  P02675
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B, C, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, C, E, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.258 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.732α = 99.58
b = 99.302β = 101.46
c = 120.732γ = 92.36
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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: Non-polymer description, Version format compliance
  • Version 1.3: 2017-03-08
    Type: Derived calculations