9AV9

R2-state HbG-Makassar hemoglobin

  • Classification: OXYGEN TRANSPORT
  • Organism(s): Homo sapiens
  • Expression System: Mus musculus
  • Mutation(s): Yes 

  • Deposited: 2024-03-01 Released: 2024-12-11 
  • Deposition Author(s): Feliciano, P.R., Lee, S.J.
  • Funding Organization(s): Department of Energy (DOE, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

Installation of HbG- Makassar by base editing restores hemoglobin function: a transformative therapy for sickle cell disease

Kostamo, Z., Ortega, M.A.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha
A, C
141Homo sapiensMutation(s): 0 
Gene Names: HBA1, HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
PHAROS:  P69905
GTEx:  ENSG00000188536 ENSG00000206172 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69905
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta
B, D
146Homo sapiensMutation(s): 1 
Gene Names: HBB
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
PHAROS:  P68871
GTEx:  ENSG00000244734 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68871
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
G [auth A],
H [auth B],
K [auth C],
M [auth D]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
GOL
Query on GOL
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth C],
J [auth C],
L [auth D]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.566α = 90
b = 58.962β = 90
c = 171.586γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0012704
Department of Energy (DOE, United States)United StatesKP1605010
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM133893

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release