4L7Y

Deoxygenated Hb in complex with the allosteric effectors, IRL2500 and 2,3-DPG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Novel small molecule modulators of human hemoglobin oxygen binding identified by small molecule microarray screening

Safo, M.K.Chowdhury, N.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha
A, C
141Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
PHAROS:  P69905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69905
Sequence Annotations
Expand
  • 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): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MH0
Query on MH0

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
H [auth C],
I [auth D]
Mesoheme
C34 H36 Fe N4 O4
CKMCSMAXNUVLQI-RGGAHWMASA-N
IRL
Query on IRL

Download Ideal Coordinates CCD File 
G [auth B](2R)-2-({(2S)-3-(biphenyl-4-yl)-2-[(3,5-dimethylbenzoyl)(methyl)amino]propanoyl}amino)-3-(1H-indol-3-yl)propanoic acid (non-preferred name)
C36 H35 N3 O4
UZDORQWMYRRLQV-SAIUNTKASA-N
DG2
Query on DG2

Download Ideal Coordinates CCD File 
J [auth D],
K [auth D]
(2R)-2,3-diphosphoglyceric acid
C3 H8 O10 P2
XOHUEYCVLUUEJJ-UWTATZPHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.75α = 90
b = 98.23β = 90
c = 65.34γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Other
  • Version 1.2: 2016-07-27
    Changes: Non-polymer description
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description