1RE3	Blood Clotting	date	Nov 06, 2003
title	Crystal Structure Of Fragment D Of Bbetad398a Fibrinogen Wit Peptide Ligand Gly-His-Arg-Pro-Amide
authors	M.S.Kostelansky, L.Betts, O.V.Gorkun, S.T.Lord
compound		source
Molecule: Fibrinogen Alphaalpha-E Chain Chain: A, D Fragment: Fragment D Of Fibrinogen Alpha Chain 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: Cho Expression_system_organ: Ovary Expression_system_vector_type: Plasmid Expression_system_plasmid: Pmlp
Molecule: Fibrinogen Beta Chain Chain: B, E Fragment: Fragment D Of Bbetad398a Fibrinogen Beta Chain Engineered: Yes Mutation: 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: Cho Expression_system_organ: Ovary Expression_system_vector_type: Plasmid Expression_system_plasmid: Pmlp
Molecule: Fibrinogen Gamma Chain Chain: C, F Fragment: Fragment D Of Fibrinogen Gamma Chain Synonym: Pro2061 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: Cho Expression_system_organ: Ovary Expression_system_vector_type: Plasmid Expression_system_plasmid: Pmlp
Molecule: Ghrp Peptide Chain: G, H Engineered: Yes		Synthetic: Yes Other_details: The Peptide Was Chemically Synthesized.
symmetry	Space Group: P 21 21 21	R_factor 0.222 R_Free 0.263
crystal cell	length a length b length c angle alpha angle beta angle gamma 54.514 147.665 229.716 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.45 Å
ligand	CA, NAG	enzyme
related structures	by homologous chain: 1FIC, 1FZC, 1FZG
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	BbetaGlu397 and BbetaAsp398 but not BbetaAsp432 are required for "B:b" interactions., Kostelansky MS, Bolliger-Stucki B, Betts L, Gorkun OV, Lord ST, Biochemistry 2004 Mar 9;43(9):2465-74. PMID:14992584

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (225 Kb) [Save to disk] Biological Unit Coordinates (1re3.pdb1.gz) 110 Kb Biological Unit Coordinates (1re3.pdb2.gz) 112 Kb LPC: Ligand-Protein Contacts for 1RE3 CSU: Contacts of Structural Units for 1RE3 Likely Quarternary Molecular Structure file(s) for 1RE3 Structure Factors (702 Kb) Retrieve 1RE3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1RE3 from S2C, [Save to disk] Re-refined 1re3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1RE3 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 1RE3

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 1RE3, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1re3a_, region A [Jmol] [rasmolscript] [script source]     - Domain d1re3b2, region B:165-199 [Jmol] [rasmolscript] [script source]     - Domain d1re3b1, region B:200-458 [Jmol] [rasmolscript] [script source]     - Domain d1re3c2, region C:106-141 [Jmol] [rasmolscript] [script source]     - Domain d1re3c1, region C:142-393 [Jmol] [rasmolscript] [script source]     - Domain d1re3d_, region D [Jmol] [rasmolscript] [script source]     - Domain d1re3e2, region E:165-199 [Jmol] [rasmolscript] [script source]     - Domain d1re3e1, region E:200-458 [Jmol] [rasmolscript] [script source]     - Domain d1e1re3, region E:82-357 [Jmol] [rasmolscript] [script source]     - Domain d1re3f2, region F:106-141 [Jmol] [rasmolscript] [script source]     - Domain d1re3f1, region F:142-393 [Jmol] [rasmolscript] [script source] Fold representative 1re3 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1re3_A] [1re3_B] [1re3_C] [1re3_D] [1re3_E] [1re3_F] [1re3_G] [1re3_H] SWISS-PROT database: [P02671] [P02675] [P02679] Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM Domain found in 1RE3: [FBG ] by SMART Alignments of the sequence of 1RE3 with the sequences similar proteins can be viewed for 1RE3'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 1RE3

Community annotation for 1RE3 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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