5KD1

Sperm whale myoglobin H64A with nitrosoamphetamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1016/j.niox.2017.04.012
  • Primary Citation of Related Structures:  
    5KD1

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myoglobin153Physeter catodonMutation(s): 2 
Gene Names: MB
EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02185
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
3QM
Query on 3QM

Download Ideal Coordinates CCD File 
G [auth A][(2R)-2-nitrosopropyl]benzene
C9 H11 N O
JNWJQOCPCZKSQI-MRVPVSSYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.5α = 90
b = 90.5β = 90
c = 45.36γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-05-17
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description