Structural analysis of monomeric hemichrome and dimeric cyanomet hemoglobins from Caudina arenicola

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 

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Structural analysis of monomeric hemichrome and dimeric cyanomet hemoglobins from Caudina arenicola.

Mitchell, D.T.Kitto, G.B.Hackert, M.L.

(1995) J Mol Biol 251: 421-431

  • DOI: https://doi.org/10.1006/jmbi.1995.0445
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The X-ray structures of two hemoglobins (Hb) from the sea cucumber Caudina arenicola (an echinoderm) have been determined: a low spin, hemichrome, monomeric Hb-C chain, and a cyanomet-liganded dimeric Hb-D chain. Attempts to obtain crystal structures of the deoxy-liganded and hemichrome forms from the same chain type have not been successful. In this work, the Hb-C chain and Hb-D chain structures are compared, and differences observed in tertiary structure related to the different ligand states for hemoglobin chains from this organism. In addition to shifts of the distal histidine and E helix, differences are noted in the position of the heme group within the heme pocket, the hydrogen bonding of the heme group to the protein, and the status of the D helix. These differences are important in understanding the ligand-linked association states of these hemoglobins. The quaternary structure of the Hb-D homodimer is compared with those from two other invertebrate hemoglobins from Scapharca inaequivalvis and Urechis caupo, which also have subunit-subunit interactions that involve the E and E' helices. The dimer interactions of the Caudina and Urechis hemoglobins are quite dissimilar. However, the dimer interface observed in cyanomet Hb-D is strikingly similar to that observed for the carbonmonoxy hemoglobin dimer from the clam, Scapharca, yet many of the key amino acid residues implicated in the cooperative mechanism of the Scapharca hemoglobin are not conserved in the Caudina hemoglobins.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Texas at Austin 78712, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEMOGLOBIN (DEOXY)158Molpadia arenicolaMutation(s): 0 
Find proteins for P80018 (Molpadia arenicola)
Explore P80018 
Go to UniProtKB:  P80018
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80018
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
C34 H32 Fe N4 O4
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.74α = 90
b = 45.23β = 104.4
c = 40.92γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-06-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other