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
crystal cell	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 Diffraction	resolution	2.80 Å
ligand	CA, NAG	enzyme
Gene Ontology	Chain Function Process Component E, B eukaryotic cell surface bind... chaperone binding platelet degranulation blood coagulation hemostasis platelet activation response to calcium ion extracellular region fibrinogen complex extracellular space plasma membrane cell cortex external side of plasma memb... platelet alpha granule platelet alpha granule lumen... blood microparticle F, C eukaryotic cell surface bind... metal ion binding platelet degranulation blood coagulation hemostasis platelet activation response to calcium ion extracellular region fibrinogen complex extracellular space plasma membrane cell cortex external side of plasma memb... platelet alpha granule platelet alpha granule lumen... blood microparticle
Primary reference	Probing 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 (492 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [2q9i_B] [2q9i_C] [2q9i_D] [2q9i_E] [2q9i_F] [2q9i_M] [2q9i_N] [2q9i_S] [2q9i_T] SWISS-PROT database: [P02671] [P02675] [P02679] Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM Domain found in 2Q9I: [FBG ] by SMART Alignments of the sequence of 2Q9I with the sequences similar proteins can be viewed for 2Q9I's classification [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2Q9I

Community annotation for 2Q9I at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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