1HLM | pdb_00001hlm

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

• PDB DOI: https://doi.org/10.2210/pdb1HLM/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Molpadia arenicola
• Mutation(s): No 


• Deposited: 1994-08-26 Released: 1995-02-07 
• Deposition Author(s): Hackert, M.L., Mitchell, D.T., Ernst, S.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Work: 
  0.190 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

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: 2049384 
• DOI: https://doi.org/10.1016/0167-4838(91)90093-f
• Primary Citation Related Structures: 
  1HLM


• 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 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.

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Organizational Affiliation: 
• Clayton Foundation Biochemical Institute, Department of Chemistry and Biochemistry, University of Texas, Austin.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.37 kDa 
• Atom Count: 1,297 
• Modeled Residue Count: 159 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMOGLOBIN (CYANO MET)	A	159	Molpadia arenicola	Mutation(s): 0
UniProt
Find proteins for P80017 (Molpadia arenicola) Explore P80017  Go to UniProtKB:  P80017

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CYN	B [auth A]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Work:  0.190 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77	α = 90
b = 77	β = 90
c = 61.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-02-07 
Deposition Author(s): Hackert, M.L., Mitchell, D.T., Ernst, S.R.

Revision History  

• Version 1.0: 1995-02-07
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary