8FB0 | pdb_00008fb0

H64Q Myoglobin in complex with acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.194 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8FB0

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Interactions of metronidazole and chloramphenicol with myoglobin: Crystal structure of a Mb-acetamide product.

Powell, S.M.Prather, K.Y.Nguyen, N.Thomas, L.M.Richter-Addo, G.B.

(2023) J Porphyr Phthalocyanines 27: 1142-1147

  • DOI: https://doi.org/10.1142/s1088424623500700
  • Primary Citation Related Structures: 
    8FB0

  • PubMed Abstract: 

    Nitroorganics present a general concern for a safe environment due to their health hazards. However, some nitroorganics such as metronidazole (Mtz) and chloramphenicol (CAM) also possess medicinal value. Mtz and CAM can undergo reductive bioactivation presumably via their nitroso derivatives. We show, using UV-vis spectroscopy, that sperm whale myoglobin (swMb) and its distal pocket mutants retaining H-bonding capacity react with Mtz in the presence of dithionite to generate products with spectra suggestive of the Fe-bound nitroso (Fe-RNO; λ max ~420 nm) forms. We have crystallized and solved the X-ray crystal structure of an H64Q swMb-acetamide compound to 1.76 Å resolution; formation of this compound results from the serendipitous crystallographic trapping, by the heme center, of acetamide from the reductive decomposition of Mtz. Only one of the swMb proteins, namely H64Q swMb with a relatively flexible Gln64 residue, reacted with CAM presumably due to the bulky nature of CAM that generally may restrict its access to the heme site.


  • Organizational Affiliation
    • Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, U.S.A. 73019.

Macromolecule Content 

  • Total Structure Weight: 18.6 kDa 
  • Atom Count: 1,526 
  • Modeled Residue Count: 153 
  • Deposited Residue Count: 154 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Myoglobin154Physeter macrocephalusMutation(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
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACM
(Subject of Investigation/LOI)

Query on ACM



Download:Ideal Coordinates CCD File
C [auth A]ACETAMIDE
C2 H5 N O
DLFVBJFMPXGRIB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.194 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.288α = 90
b = 90.288β = 90
c = 45.255γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-01
    Changes: Database references