3G4U

Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and dichloropropane bound to the XE4 cavity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis.

Knapp, J.E.Pahl, R.Cohen, J.Nichols, J.C.Schulten, K.Gibson, Q.H.Srajer, V.Royer, W.E.

(2009) Structure 17: 1494-1504

  • DOI: 10.1016/j.str.2009.09.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • As in many other hemoglobins, no direct route for migration of ligands between solvent and active site is evident from crystal structures of Scapharca inaequivalvis dimeric HbI. Xenon (Xe) and organic halide binding experiments, along with computatio ...

    As in many other hemoglobins, no direct route for migration of ligands between solvent and active site is evident from crystal structures of Scapharca inaequivalvis dimeric HbI. Xenon (Xe) and organic halide binding experiments, along with computational analysis presented here, reveal protein cavities as potential ligand migration routes. Time-resolved crystallographic experiments show that photodissociated carbon monoxide (CO) docks within 5 ns at the distal pocket B site and at more remote Xe4 and Xe2 cavities. CO rebinding is not affected by the presence of dichloroethane within the major Xe4 protein cavity, demonstrating that this cavity is not on the major exit pathway. The crystal lattice has a substantial influence on ligand migration, suggesting that significant conformational rearrangements may be required for ligand exit. Taken together, these results are consistent with a distal histidine gate as one important ligand entry and exit route, despite its participation in the dimeric interface.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, The University of Massachusetts Medical School, Worcester, MA 01605, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLOBIN-1
A, B
146Anadara inaequivalvisMutation(s): 0 
Find proteins for P02213 (Anadara inaequivalvis)
Go to UniProtKB:  P02213
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0CL
Query on 0CL

Download SDF File 
Download CCD File 
A, B
1,3-dichloropropane
C3 H6 Cl2
YHRUOJUYPBUZOS-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO

Download SDF File 
Download CCD File 
A, B
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.170α = 90.00
b = 43.830β = 121.88
c = 83.430γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description