3IC0 | pdb_00003ic0

Crystal Structure of liganded hemoglobin in complex with a potent antisickling agent, INN-298

• PDB DOI: https://doi.org/10.2210/pdb3IC0/pdb

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


• Deposited: 2009-07-17 Released: 2009-07-28 
• Deposition Author(s): Safo, M.K., Musayev, F.N., Gandhi, A.K., Jorge, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Structural and in Vitro Chracterization of Pridyl Derivatives of Benzaldehydes: Highly Potent Antisickling Agents

Osheiza, A., Mohini, G., Ijoema, N., Amit, K.G., Faik, N.M., Richmond, D.-D., Toshio, A., Martin, K.S.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 65.78 kDa 
• Atom Count: 5,057 
• Modeled Residue Count: 574 
• Deposited Residue Count: 574 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A, C	141	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905  Go to UniProtKB:  P69905
PHAROS:  P69905 GTEx:  ENSG00000188536 ENSG00000206172

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D	146	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871  Go to UniProtKB:  P68871
PHAROS:  P68871 GTEx:  ENSG00000244734

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	F [auth A], J [auth B], L [auth C], Q [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
B77	G [auth A], H [auth A], M [auth C], N [auth C]	2-[(2-methoxy-5-methylphenoxy)methyl]pyridine C14 H15 N O2 AVXQTLSOXWQOHO-UHFFFAOYSA-N
SO4	O [auth C], R [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
OXY	E [auth A], I [auth B], K [auth C], P [auth D]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.978	α = 90
b = 91.978	β = 90
c = 143.942	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Safo, M.K., Musayev, F.N., Gandhi, A.K., Jorge, P.

Revision History  

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2019-11-27
  Changes: Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary