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 Diffractionresolution 2.45 Å
ligand CA, NAG enzyme
related structures by homologous chain: 1FIC, 1FZC, 1FZG
Primary referenceBbetaGlu397 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 (768 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.
  • 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_D] [1re3_G] [1re3_C] [1re3_B] [1re3] [1re3_F] [1re3_H] [1re3_E] [1re3_A]
  • SWISS-PROT database: [P02671] [P02675] [P02679]
  • Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM
  • Domain found in 1RE3: [FBG ] by SMART
  • Other resources with information on 1RE3
  • Community annotation for 1RE3 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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