1HLM

AMINO ACID SEQUENCE OF A GLOBIN FROM THE SEA CUCUMBER CAUDINA (MOLPADIA) ARENICOLA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Amino acid sequence of a globin from the sea cucumber Caudina (Molpadia) arenicola.

Mauri, F.Omnaas, J.Davidson, L.Whitfill, C.Kitto, G.B.

(1991) Biochim.Biophys.Acta 1078: 63-67


  • PubMed Abstract: 
  • Coelomic cells from the sea cucumber Caudina (Molpadia) arenicola contain four major globins, A, B, C and D. The hemoglobins from this organism show unusual ligand-linked dissociation properties. The complete amino acid sequence of the D globin has b ...

    Coelomic cells from the sea cucumber Caudina (Molpadia) arenicola contain four major globins, A, B, C and D. The hemoglobins from this organism show unusual ligand-linked dissociation properties. The complete amino acid sequence of the D globin has been established. It is N-acetylated, consists of 158 residues and has a 10 amino acid N-terminal extension similar to that found in some other invertebrate globins. The C. arenicola D globin has an equal sequence identity (28%) with both alpha and beta human globins and as anticipated, is more closely related to these vertebrate proteins than are molluscan globins. The C. arenicola D globin shows a 59% identity with the globin I from the sea cucumber Paracaudina chilensis. The availability of the C. arenicola D globin sequence will aid the X-ray analysis of this protein and facilitate an understanding of the changes in subunit interactions that occur with cooperative ligand binding.


    Related Citations: 
    • Preliminary Crystallographic Data on Monomeric and Dimeric Hemoglobins from the Sea Cucumber, Molpadia Arenicola
      Carson, W.M.,Bowers, T.R.,Kitto, G.B.,Hackert, M.L.
      (1979) J.Biol.Chem. 254: 7400
    • N-Terminal Substitution of Some Sea Cucumber Hemoglobins
      Kitto, G.B.,Erwin, D.,West, R.,Omnaas, J.
      (1976) COMP.BIOCHEM.PHYSIOL. B: BIOCHEM.MOL.BIOL. 55: 105


    Organizational Affiliation

    Clayton Foundation Biochemical Institute, Department of Chemistry and Biochemistry, University of Texas, Austin.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMOGLOBIN (CYANO MET)
A
159Caudina arenicolaN/A
Find proteins for P80017 (Caudina arenicola)
Go to UniProtKB:  P80017
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYN
Query on CYN

Download SDF File 
Download CCD File 
A
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.190 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.000α = 90.00
b = 77.000β = 90.00
c = 61.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-07
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other