2Q9I Blood Clotting date Jun 12, 2007
title Crystal Structure Of D-Dimer From Human Fibrin Complexed Wit Arg-Pro-Tyr-Amide.
authors R.F.Doolittle, L.Pandi
compound source
Molecule: Fibrinogen Alpha Chain
Chain: A, D
Fragment: Unp Residues 130-216
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Fibrinogen Beta Chain
Chain: B, E
Fragment: Unp Residues 164-491

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Fibrinogen, Gamma Polypeptide
Chain: C, F
Fragment: Unp Residues 114-437
Synonym: Fibrinogen Gamma Chain, Isoform Cra_m

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Fibrin B Knob (Ghrpam)
Chain: S, T
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Humans.

Molecule: Fibrin B Knob (Mhrpyam)
Chain: M, N
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Does Not Occur Naturally.
symmetry Space Group: P 21 21 21
R_factor 0.216 R_Free 0.276
length a length b length c angle alpha angle beta angle gamma
54.380 147.230 231.480 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand CA, NAG enzyme
A, D

E, B

F, C

Primary referenceProbing the beta-chain hole of fibrinogen with synthetic peptides that differ at their amino termini., Doolittle RF, Pandi L, Biochemistry. 2007 Sep 4;46(35):10033-8. Epub 2007 Aug 10. PMID:17688324
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (207 Kb) [Save to disk]
  • Biological Unit Coordinates (2q9i.pdb1.gz) 104 Kb
  • Biological Unit Coordinates (2q9i.pdb2.gz) 100 Kb
  • LPC: Ligand-Protein Contacts for 2Q9I
  • CSU: Contacts of Structural Units for 2Q9I
  • Likely Quarternary Molecular Structure file(s) for 2Q9I
  • Structure Factors (498 Kb)
  • Retrieve 2Q9I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Q9I from S2C, [Save to disk]
  • Re-refined 2q9i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Q9I 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 2Q9I
  • 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 2Q9I, from MSDmotif at EBI
  • Fold representative 2q9i from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2q9i_B] [2q9i_M] [2q9i_E] [2q9i_F] [2q9i_D] [2q9i_C] [2q9i_A] [2q9i_T] [2q9i] [2q9i_S] [2q9i_N]
  • SWISS-PROT database: [P02671] [P02675] [P02679]
  • Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM
  • Domain found in 2Q9I: [FBG ] by SMART
  • Other resources with information on 2Q9I
  • Community annotation for 2Q9I 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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