ISDA: 2W6V

Deposition Date 2008-12-19

Release Date 2009-04-28

Last Version Date 2025-10-01

Entry Detail

PDB ID:

2W6V

Keywords:

OXYGEN TRANSPORT

Title:

Structure of Human deoxy Hemoglobin A in complex with Xenon

Biological Source:

Source Organism:

HOMO SAPIENS (Taxon ID: 9606)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.80 Å

R-Value Free:

0.21

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 1 21 1

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:HEMOGLOBIN SUBUNIT ALPHA
Gene (Uniprot):HBA1, HBA2
Chain IDs:A, C
Chain Length:141
Number of Molecules:2
Biological Source:HOMO SAPIENS

UniProt ID:P69905 Pfam ID:PF00042

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:HEMOGLOBIN SUBUNIT BETA
Gene (Uniprot):HBB
Chain IDs:B, D
Chain Length:146
Number of Molecules:2
Biological Source:HOMO SAPIENS

UniProt ID:P68871 Pfam ID:PF00042

Ligand Molecules

GOL

HEM

PO4

SO4

Primary Citation

Pattern of Cavities in Globins: The Case of Human Hemoglobin.

Savino, C, Miele, A.E, Draghi, F, Johnson, K.A, Sciara, G, Brunori, M, Vallone, B.Show

Biopolymers 91 1097 ? (2009)

PMID: 19365817 DOI: 10.1002/BIP.21201

Abstact

Our aim is to shed light on the conservation of potential ligand docking sites that play an important role in ligand dynamics of globins by using the technique of filling internal cavities naturally present in hemoglobin and myoglobin with xenon atoms. In particular, we present the high resolution structures of the Xe-adduct of deoxygenated wild type human hemoglobin and a quadruple mutant (L(B10)Y and H(E7)Q in alpha and beta chains). For the sake of comparison we also determined under the same experimental conditions the xenon complex of wild type sperm whale myoglobin. The analysis revealed that the number and position of Xe binding cavities are different in the alpha and beta subunits, the latter being more similar to myoglobin. Notably, no proximal Xe docking site was detected in hemoglobin, at variance with myoglobin. The pattern of internal cavities accessibility and affinity for xenon suggests a different role for the dynamics of ligand migration in the two types of hemoglobin chains as compared to myoglobin. The number and position of hydrophobic cavities in hemoglobin are briefly discussed also in comparison with the data available for other members of the globin superfamily.

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