3WHM | pdb_00003whm

Structure of Hemoglobin Complex with 18-crown-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.253 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view detailsBest fitted O4BClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Crowning proteins: modulating the protein surface properties using crown ethers.

Lee, C.C.Maestre-Reyna, M.Hsu, K.C.Wang, H.C.Liu, C.I.Jeng, W.Y.Lin, L.L.Wood, R.Chou, C.C.Yang, J.M.Wang, A.H.

(2014) Angew Chem Int Ed Engl 53: 13054-13058

  • DOI: https://doi.org/10.1002/anie.201405664
  • Primary Citation of Related Structures:  
    3WH0, 3WHM, 3WUR

  • PubMed Abstract: 

    Crown ethers are small, cyclic polyethers that have found wide-spread use in phase-transfer catalysis and, to a certain degree, in protein chemistry. Crown ethers readily bind metallic and organic cations, including positively charged amino acid side chains. We elucidated the crystal structures of several protein-crown ether co-crystals grown in the presence of 18-crown-6. We then employed biophysical methods and molecular dynamics simulations to compare these complexes with the corresponding apoproteins and with similar complexes with ring-shaped low-molecular-weight polyethylene glycols. Our studies show that crown ethers can modify protein surface behavior dramatically by stabilizing either intra- or intermolecular interactions. Consequently, we propose that crown ethers can be used to modulate a wide variety of protein surface behaviors, such as oligomerization, domain-domain interactions, stabilization in organic solvents, and crystallization.


  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529 (Taiwan); Core Facilities for Protein Structural Analysis, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529 (Taiwan).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alphaA,
C [auth E]
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit betaB,
D [auth F]
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth E],
O [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
O4B
Query on O4B

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth E],
M [auth E],
P [auth F]
1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE
C12 H24 O6
XEZNGIUYQVAUSS-UHFFFAOYSA-N
OXY
Query on OXY

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
N [auth E]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.158α = 90
b = 104.638β = 108.69
c = 59.957γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view detailsBest fitted O4BClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2019-07-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.2: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Refinement description