3D1M Signaling Protein Cell Adhesion date May 06, 2008
title Crystal Structure Of Sonic Hedgehog Bound To The Third Fniii Cdo
authors J.S.Mclellan, D.J.Leahy
compound source
Molecule: Sonic Hedgehog Protein
Chain: A, B
Fragment: N-Terminal Domain, Sonic Hedgehog Protein N-Produ Residues 26-189;
Synonym: Shh, Hhg-1, Sonic Hedgehog Protein N-Product, Soni Protein C-Product;
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Shh, Hhg1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Cell Adhesion Molecule
Chain: C, D
Fragment: Fibronectin Type-III Domain 3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdon, Cdo
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.186 R_Free 0.229
length a length b length c angle alpha angle beta angle gamma
71.179 98.582 144.047 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand CA, ZN enzyme
A, B

D, C

Primary referenceThe mode of Hedgehog binding to Ihog homologues is not conserved across different phyla., McLellan JS, Zheng X, Hauk G, Ghirlando R, Beachy PA, Leahy DJ, Nature. 2008 Sep 14. PMID:18794898
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (94 Kb) [Save to disk]
  • Biological Unit Coordinates (3d1m.pdb1.gz) 46 Kb
  • Biological Unit Coordinates (3d1m.pdb2.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 3D1M
  • CSU: Contacts of Structural Units for 3D1M
  • Likely Quarternary Molecular Structure file(s) for 3D1M
  • Structure Factors (833 Kb)
  • Retrieve 3D1M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D1M from S2C, [Save to disk]
  • Re-refined 3d1m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D1M 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 3D1M
  • 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 3D1M, from MSDmotif at EBI
  • Fold representative 3d1m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d1m_A] [3d1m_D] [3d1m] [3d1m_B] [3d1m_C]
  • SWISS-PROT database: [Q4KMG0] [Q62226]
  • Domain organization of [CDON_HUMAN] [SHH_MOUSE] by SWISSPFAM
  • Domain found in 3D1M: [FN3 ] by SMART
  • Other resources with information on 3D1M
  • Community annotation for 3D1M 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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