The Open Protein Structure Annotation Network
PDB Keyword


    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of NITROREDUCTASE FAMILY PROTEIN (YP_001089872.1) from CLOSTRIDIUM DIFFICILE 630 at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 3h4o Target Id 391667
    Related PDB Ids 3koq 
    Molecular Characteristics
    Source Clostridium difficile 630
    Alias Ids TPS14650,YP_001089872.1,, 85755 Molecular Weight 19735.69 Da.
    Residues 172 Isoelectric Point 5.54
    Sequence mnfvelakkryscrnyqdrkvekeklekvldvariaptggnrqpqrliviqekeginklskaaniydap lailvcgdkdkvwtrpfdgkqltdidtsivtdhmmlqatelglasvwvcyfnpdiireefslpdnlepi nillmgyeskipesperhektrvplseivsyetl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.50 Rfree 0.167
    Matthews' coefficent 2.32 Rfactor 0.139
    Waters 296 Solvent Content 46.89

    Ligand Information


    Google Scholar output for 3h4o

    Protein Summary

    The gene CD3355 from Clostridium difficile 630 encodes the YP_001089872 protein with 172 residues . It has been annotated as a putative nitroreductase belonging to Nitroreductase Pfam family PF00881. The protein is present as a monomer in the asymmetric unit of the unit cell of the crystal structure (Fig. 1), and packing analysis suggests that the dimer with symmetry mate (cyan and light blue) is the relevant oligomeric form in solution. In the putative active site of the protein, an MPD and a FMN (red sticks) are found. The FMN restraints dictionary was modified to allow bending of the isoalloxazine ring along the N5-N10 virtual axis resulting in an improved fit between the FMN coordinates and electron density.

    SCOP classifies 3koq in the alpha+beta class, FMN-dependent nitroreductase-like superfamily. Other protein structures that are most similar in structure (by DALI) to 3koq are PDB:3e10 (putative NADH oxidase, Z=20.0, 1.9A rmsd, 157 Ca aligned, 32% id, topsan-3e10), PDB:3e39 (putative nitroreductase, Z=20.0, 2.3A rmsd, 160 Ca aligned, 24% id, topsan-3e39), PDB:3g14 (nitroreductase family protein, Z=19.1, 1.6A rmsd, 145 Ca aligned, 29% id, topsan-3g14), PDB:2b67 (nitroreductase, Z=19.1, 1.9A rmsd, 159 Ca aligned, 25% id), PDB:3bem (putative NAD(P)H nitroreductase YDFN, Z=18.9, 2.2A rmsd, 162 Ca aligned, 23% id, topsan-3bem). All the above except 3g14 structure have bound FMN. The superposition of 3koq with 3g14 indicates that the loop (residues 157-163 of 3koq; left side in the below Fig. 3), containing important interacting residues to FMN, is missing in the 3g14 structure.



    Fig.1. Crystal structure of 3koq in the asymmetric unit. 


    Fig. 2. Biomolecule of 3koq.




    Fig. 3. Superposition of 3koq (light blue) to 3g14 (wheat color). The FMN and MPD of 3koq are shown in red. The FMN interacting residues of 3koq are Arg10, Ser12, Arg14, Tyr66, Cys118, Tyr119, Glu151 and Arg155. The corresponding residues in the 3g14 structure are Arg10, Ser12, Lys14, Ala73, Ala125, Ala126 (and two missing residues).


      Comparison between Crystal Form1 (3h4o) and 2 (3koq)








    Crystal Form1

    Crystal Form2

    Crystal ID



    Space Group


    77.9,63.5,55.5,beta=131.11 deg


    58.4, 87.9, 87.5, beta=102.33 deg





    Dimer (AA’)

    Dimer (AB and CD)




    Ligand modeled near FMN


    Amol: Cl

    Bmol: GOL


    Dmol: Cl

    Structural Difference

    Conformational changes in the loop after H4 (residues 146-150)

    Ligand Summary

    A MPD and a FMN are modeled in the active site.




    No references found.

    Tag page
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch