7UF7

Crystal structure of liganded Hb with the 5-HMF analog, MMA503

  • Classification: OXYGEN TRANSPORT
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2022-03-22 Released: 2022-03-30 
  • Deposition Author(s): Donkor, A.K., Musayev, F.N., Safo, M.K.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Improving the antisickling activity of furaldehyde

El-Araby, M.E., Omar, A.M., Ghatge, M.S., Musayev, F.N., Donkor, A.K., Paredes, S.D., Abdulmalik, O., Safo, M.K.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha
A, C
142Homo 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
147Homo sapiensMutation(s): 0 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
M [auth D]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
N2Q (Subject of Investigation/LOI)
Query on N2Q
Download Ideal Coordinates CCD File 
G [auth A],
L [auth C]		(5P)-5-(5-methylfuran-2-yl)-1H-pyrazole
C8 H8 N2 O
ZIJASYNQNLPMPY-UHFFFAOYSA-N
CMO (Subject of Investigation/LOI)
Query on CMO
Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
K [auth C],
N [auth D]		CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.614α = 90
b = 83.12β = 90
c = 105.122γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR61HL156158
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesS10OD021756

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description