1M1J Blood Clotting date Jun 19, 2002
title Crystal Structure Of Native Chicken Fibrinogen With Two Diff Bound Ligands
authors Z.Yang, J.M.Kollman, L.Pandi, R.F.Doolittle
compound source
Molecule: Fibrinogen Alpha Subunit
Chain: A, D
 Organism_scientific: Gallus Gallus
Organism_common: Chicken
Organism_taxid: 9031
Tissue: Blood

Molecule: Fibrinogen Beta Chain
Chain: B, E
Organism_scientific: Gallus Gallus
Organism_common: Chicken
Organism_taxid: 9031
Tissue: Blood

Molecule: Fibrinogen Gamma Chain
Chain: C, F
Organism_scientific: Gallus Gallus
Organism_common: Chicken
Organism_taxid: 9031
Tissue: Blood

Molecule: Gly-Pro-Arg-Pro Peptide
Chain: G, H
Engineered: Yes
Synthetic: Yes
Other_details: The Peptide Is Chemically Synthesized.

Molecule: Gly-His-Arg-Pro Peptide
Chain: I, J
Engineered: Yes
Synthetic: Yes
Other_details: The Peptide Is Chemically Synthesized.
symmetry Space Group: P 1 21 1
R_factor 0.227 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
114.090 100.020 200.090 90.00 105.79 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand CA, NAG, NDG enzyme
note 1M1J (Molecule of the Month:pdb83)supersedes 1JFE
related structures by homologous chain: 1FZF, 1RE4
Gene
Ontology
ChainFunctionProcessComponent
A, D


E, B


F, C


Primary referenceCrystal structure of native chicken fibrinogen at 2.7 A resolution., Yang Z, Kollman JM, Pandi L, Doolittle RF, Biochemistry 2001 Oct 23;40(42):12515-23. PMID:11601975
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (332 Kb) [Save to disk]
  • Biological Unit Coordinates (1m1j.pdb1.gz) 323 Kb
  • LPC: Ligand-Protein Contacts for 1M1J
  • CSU: Contacts of Structural Units for 1M1J
  • Likely Quarternary Molecular Structure file(s) for 1M1J
  • Retrieve 1M1J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1M1J from S2C, [Save to disk]
    • View 1M1J 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 1M1J
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1M1J, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m1ja_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1m1jb1, region B:200-464 [Jmol] [rasmolscript] [script source]
        - Domain d1m1jb2, region B:63-199 [Jmol] [rasmolscript] [script source]
        - Domain d1m1jc1, region C:142-393 [Jmol] [rasmolscript] [script source]
        - Domain d1m1jc2, region C:4-141 [Jmol] [rasmolscript] [script source]
        - Domain d1m1jd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1m1je1, region E:200-463 [Jmol] [rasmolscript] [script source]
        - Domain d1m1je2, region E:63-199 [Jmol] [rasmolscript] [script source]
        - Domain d1m1jf1, region F:142-393 [Jmol] [rasmolscript] [script source]
        - Domain d1m1jf2, region F:5-141 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1m1j_B] [1m1j_E] [1m1j_C] [1m1j_F] [1m1j_I] [1m1j_G] [1m1j] [1m1j_A] [1m1j_J] [1m1j_H] [1m1j_D]
  • SWISS-PROT database: [P14448] [Q02020] [O93568]
  • Domain organization of [FIBA_CHICK] [FIBB_CHICK] [O93568_CHICK] by SWISSPFAM
  • Domains found in 1M1J: [FBG] [Fib_alpha ] by SMART
    • Other resources with information on 1M1J
  • Community annotation for 1M1J 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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