Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 67.75 kDa 
• Atom Count: 6,291 
• Modelled Residue Count: 574 
• Deposited Residue Count: 574 
• Unique protein chains: 3

 2W72

DEOXYGENATED STRUCTURE OF A DISTAL SITE HEMOGLOBIN MUTANT PLUS XE

• PDB DOI: 10.2210/pdb2W72/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-12-19 Released: 2009-04-28 
• Deposition Author(s): Miele, A.E., Draghi, F., Sciara, G., Johnson, K.A., Renzi, F., Vallone, B., Brunori, M., Savino, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.07 Å
• R-Value Free: 0.153 
• R-Value Work: 0.129 
• R-Value Observed: 0.130 

Literature

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.

(2009) Biopolymers 91: 1097

• PubMed: 19365817 
• DOI: 10.1002/bip.21201
• Primary Citation of Related Structures:  
  2W6V, 2W6W, 2W72


• PubMed Abstract: 
  

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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Organizational Affiliation: 

University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN HEMOGLOBIN A	A	141	Homo sapiens	Mutation(s): 2  Gene Names: HBA1, HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905  Go to UniProtKB:  P69905
PHAROS:  P69905

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN HEMOGLOBIN A	B, D	146	Homo sapiens	Mutation(s): 2  Gene Names: HBB
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871  Go to UniProtKB:  P68871
PHAROS:  P68871

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN HEMOGLOBIN A	C	141	Homo sapiens	Mutation(s): 2  Gene Names: HBA1, HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905  Go to UniProtKB:  P69905
PHAROS:  P69905

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], FA [auth D], P [auth B], V [auth C]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
XE	AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], HA [auth D], I [auth A], IA [auth D], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], T [auth B], U [auth B]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N
SO4	F [auth A], G [auth A], GA [auth D], H [auth A], Q [auth B], R [auth B], W [auth C], X [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	Y [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	O [auth A], S [auth B], Z [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.07 Å
• R-Value Free: 0.153 
• R-Value Work: 0.129 
• R-Value Observed: 0.130 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.957	α = 90
b = 82.447	β = 99.6
c = 53.531	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-28 
Deposition Author(s): Miele, A.E., Draghi, F., Sciara, G., Johnson, K.A., Renzi, F., Vallone, B., Brunori, M., Savino, C.

Revision History  

• Version 1.0: 2009-04-28
  Type: Initial release
  
• Version 1.1: 2011-08-17
  Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Derived calculations
• Version 1.3: 2023-03-08
  Changes: Database references, Derived calculations, Other