5KD1

Sperm whale myoglobin H64A with nitrosoamphetamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Nitrosoamphetamine binding to myoglobin and hemoglobin: Crystal structure of the H64A myoglobin-nitrosoamphetamine adduct.

Wang, B.Powell, S.M.Guan, Y.Xu, N.Thomas, L.M.Richter-Addo, G.B.

(2017) Nitric Oxide 67: 26-29

  • DOI: 10.1016/j.niox.2017.04.012

  • PubMed Abstract: 
  • N-hydroxyamphetamine (AmphNHOH) is an oxidative metabolite of amphetamine and methamphetamine. It is known to form inhibitory complexes upon binding to heme proteins. However, its interactions with myoglobin (Mb) and hemoglobin (Hb) have not been rep ...

    N-hydroxyamphetamine (AmphNHOH) is an oxidative metabolite of amphetamine and methamphetamine. It is known to form inhibitory complexes upon binding to heme proteins. However, its interactions with myoglobin (Mb) and hemoglobin (Hb) have not been reported. We demonstrate that the reactions of AmphNHOH with ferric Mb and Hb generate the respective heme-nitrosoamphetamine derivatives characterized by UV-vis spectroscopy. We have determined the X-ray crystal structure of the H64A Mb-nitrosoamphetamine complex to 1.73 Å resolution. The structure reveals the N-binding of the nitroso-d-amphetamine isomer, with no significant H-bonding interactions between the ligand and the distal pocket amino acid residues.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, University of Oklahoma, Norman, OK 73019, United States. Electronic address: grichteraddo@ou.edu.,Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, University of Oklahoma, Norman, OK 73019, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A
153Physeter macrocephalusMutation(s): 2 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
Go to Gene View: MB
Go to UniProtKB:  P02185
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
3QM
Query on 3QM

Download SDF File 
Download CCD File 
A
[(2R)-2-nitrosopropyl]benzene
2-nitroso-1-phenylpropane
C9 H11 N O
JNWJQOCPCZKSQI-MRVPVSSYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 90.500α = 90.00
b = 90.500β = 90.00
c = 45.360γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
iMOSFLMdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesCHE-1213674

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-05-17
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence
  • Version 1.3: 2017-11-01
    Type: Author supporting evidence