2FFD Blood Clotting date Dec 19, 2005
title Fibrinogen Fragment D With "A" Knob Peptide Mimic Gprvve
authors L.Betts
compound source
Molecule: Fibrinogen Alphaalpha-E Chain
Chain: A, D
Fragment: Residues 145-210
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fga
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Ovary Cells

Molecule: Fibrinogen Beta Chain
Chain: B, E
Fragment: Residues 179-491
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fgb
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Ovary Cells

Molecule: Fibrinogen Gamma Chain
Chain: C, F
Fragment: Residues 122-432
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fgg
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Ovary Cells

Molecule: Gly-Pro-Arg-Val-Val-Glu Peptide
Chain: G, H, I, J
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Construct
symmetry Space Group: P 21 21 21
R_factor 0.211 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
89.521 94.652 227.490 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.89 Å
ligand CA, FUC, NAG enzyme
Primary referenceThe structure of fibrinogen fragment D with the 'A' knob peptide GPRVVE., Betts L, Merenbloom BK, Lord ST, J Thromb Haemost. 2006 May;4(5):1139-41. PMID:16689770
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (225 Kb) [Save to disk]
  • Biological Unit Coordinates (2ffd.pdb1.gz) 113 Kb
  • Biological Unit Coordinates (2ffd.pdb2.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 2FFD
  • CSU: Contacts of Structural Units for 2FFD
  • Likely Quarternary Molecular Structure file(s) for 2FFD
  • Structure Factors (335 Kb)
  • Retrieve 2FFD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2FFD from S2C, [Save to disk]
  • Re-refined 2ffd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2FFD in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2FFD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2FFD, from MSDmotif at EBI
  • Fold representative 2ffd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ffd_J] [2ffd_C] [2ffd_E] [2ffd_H] [2ffd_G] [2ffd_D] [2ffd_B] [2ffd_F] [2ffd] [2ffd_I] [2ffd_A]
  • SWISS-PROT database: [P02671] [P02675] [P02679]
  • Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM
  • Domain found in 2FFD: [FBG ] by SMART
  • Other resources with information on 2FFD
  • Community annotation for 2FFD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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