.
The Open Protein Structure Annotation Network
PDB Keyword
.

3cu3

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

    Title Crystal structure of Domain of Unknown Function with a Cystatin-like Fold (ZP_00107529.1) from Nostoc punctiforme PCC 73102 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3cu3 Target Id 377910
    Molecular Characteristics
    Source Nostoc punctiforme pcc 73102
    Alias Ids TPS1698,NPUN_22DEC03_CONTIG1_REVISED_GENENPR1993, 3.10.450.50 Molecular Weight 19138.48 Da.
    Residues 171 Isoelectric Point 5.06
    Sequence mnlqtdqttttadesairafhrqmidawnrgsgegfaapfsetadfitfegthlkgrkeiaafhqqafd tvvkgtrlegevdfvrfvnsqlalmlvvirvilpgqtetsasrdslplyvvtkgdegwqiegllntrkl tlerqfflddfdslsaeaqrqvtdlvaslkqsh
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.216
    Matthews' coefficent 2.76 Rfactor 0.161
    Waters 147 Solvent Content 55.38

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3cu3
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Dimensionality reduction in computational demarcation of protein tertiary structures
    RR Joshi, PR Panigrahi, RN Patil - Journal of Molecular Modeling, 2011 - Springer
     

    Protein Summary

    Gene Npun_R1993 from Nostoc punctiforme pcc 73102 encodes the YP_001865572 amino acid sequence annotated as NTF2-like superfamily member.

    SCOP classifies 3cu3 in the alpha+beta class, NTF2-like superfamily, BaiE/LinA-like family.

    Dali search with 3cu3 as query provides as top hits the NTF2-like proteins PDB:3gzr and PDB:2rgq (Z=18), a putative ketosteroid isomerase PDB:3hx8 (Z=16), and the uncharacterized protein PDB:3b8l (Z=15).

    FFAS and structural alignment from SSM searches, provide the structures PDB:1hkx (Z=13) and PDB:2ux0 (Z=13) as highly similar to 3cu3. The biomolecule of 3cu3 has been suggested as a dimer according to the SEC data and the calculation of interface interaction (PISA). The dimer interface is formed by sticking together two C-terminal helices (orange in Figure 1) like the middle and index finger of the left and right hand showing a 'V'. The magnesium ion is located in the loop connecting the two C-terminal helices. It is surrounded by water molecules which in turn are coordinated by residue Glu-80, and the carbonyl oxygens of residues Leu-152, Asp-150 from a crystallographically symmetric chain. Comparison of this structure to PDB:2chc (Z=15) shows that the C-terminus in 2chc is packed against the same protein chain and does not participate in dimerization. Since an ethylene glycole molecule is very close to the Mg2+ ion it may be speculated that this molecule and ion substitute for a ligand with a positively charged group.

    Mg2+ ion, ethylene glycol and polyethylene glycol are modeled in the structure.

     

    3cu3.png    377910_Figure_2.png

    Figure 1. The 3cuc monomer structure.                        Figure 2.  The biomolecule of 3cuc may be a dimer.




    Figure 3. The superposing of 3cuc with 1HKX (green) and 2UXO (yellow).
     

    Ligand Summary



    References

    Reviews

    References

     

    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