1EDM Coagulation Factor date Mar 21, 1996
title Epidermal Growth Factor-Like Domain From Human Factor Ix
authors Z.Rao, P.Handford, M.Mayhew, V.Knott, G.G.Brownlee, D.Stuart
compound source
Molecule: Factor Ix
Chain: B, C
Fragment: Epidermal Growth Factor-Like Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Rz1032, Xl1-Blue, Mc1061
Gene: Human Factor Ix
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pma91
Expression_system_gene: Human Factor Ix
symmetry Space Group: P 43 21 2
R_factor 0.157 R_Free NULL
length a length b length c angle alpha angle beta angle gamma
40.300 40.300 98.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.50 Å
ligand CA enzyme
note 1EDM is a representative structure
C, B

Primary referenceThe structure of a Ca(2+)-binding epidermal growth factor-like domain: its role in protein-protein interactions., Rao Z, Handford P, Mayhew M, Knott V, Brownlee GG, Stuart D, Cell 1995 Jul 14;82(1):131-41. PMID:7606779
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (21 Kb) [Save to disk]
  • Biological Unit Coordinates (1edm.pdb1.gz) 17 Kb
  • LPC: Ligand-Protein Contacts for 1EDM
  • CSU: Contacts of Structural Units for 1EDM
  • Likely Quarternary Molecular Structure file(s) for 1EDM
  • Retrieve 1EDM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1EDM from S2C, [Save to disk]
  • View 1EDM 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 1EDM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1EDM 1EDMB 1EDMC from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1EDM, from MSDmotif at EBI
  • Genome occurence of 1EDM's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1edmb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1edmc_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1edm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1edm] [1edm_C] [1edm_B]
  • SWISS-PROT database: [P00740]
  • Domain organization of [FA9_HUMAN] by SWISSPFAM
  • Domain found in 1EDM: [EGF_CA ] by SMART
  • Other resources with information on 1EDM
  • Community annotation for 1EDM 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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