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

    Title Crystal structure of Putative phosphohydrolase (YP_929327.1) from Shewanella amazonensis SB2B at 1.62 A resolution. To be Published
    Site JCSG
    PDB Id 3m1t Target Id 394107
    Molecular Characteristics
    Source Shewanella amazonensis sb2b
    Alias Ids TPS26607,YP_929327.1, _0037.000821_, 326250 Molecular Weight 29398.32 Da.
    Residues 274 Isoelectric Point 5.31
    Sequence mhsaallqkvdelprlpkaiaelldvvnnedstvkavseklshdpvlsarvlrlansarfgcsrevgti ddavvrlgmqtlrtlviasavvgavpkvegfdladfwgntfevaiicqelakrlgtlpeeaftcgilhs igellivngdpavaatisaavadgadrnlmekellgydnaeigallaqswkftphlvkgiqfqnhpksa epysklagmlamakqiaadwdkipddertswlaqinilagikvdlgglaeklakmhgqgmemgkqla
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.62 Rfree 0.201
    Matthews' coefficent 2.93 Rfactor 0.182
    Waters 247 Solvent Content 57.98

    Ligand Information


    Google Scholar output for 3m1t

    Protein Summary

    [The following content, including  figures, is uploaded from Kevin Kai Jin's refinement summary, more discussion about this protein structure will be available very soon]


    Pfam:  matches the Pfam HDOD (PF08668) entry


    Gene Sama_3455 from SHEWANELLA AMAZONENSIS SB2 encodes the YP_929327 protein, which belongs to the pfam PF08668  group with members displaying phosphohydrolase activity.  The NCBI blast sequence alignment indicates that this protein contains a conserved domain belonging to HD superfamily.  

    Pre-SCOP classifies 3m1t in the all alpha class, HD-domain/PDEase-like superfamily, modified HD domain family. A structural similarity search via SSM and Dali sever show that 3m1t is structurally similar to the exopolyphosphatase (PDB 2FLO),  a putative phosphohydrolase (JCSG target PDB 3I7A) and metal-dependent phosphohydrolase (JCSG target PDB 3HC1). Differing from structure 3HC1, the corresponding residues in protein YP_929327 are varied and no metal ions are identified in the structure.  The interface interaction suggests that the biomolecule of 3m1t is likely a dimer.



    Figure 1. The structure of 3m1t mainly consists of helices.






    Figure 2. The probable biomolecule of 3m1t is a dimer.



    Figure 3. Protein 3M1T (Green) is structurally similar

    to 3HC1(cyan), and 3I7A(magenta). 



    Figure 4. Protein 3HC1(JCSG target) is a metal-(Fe)-dependent





    Figure 5. Corresponding metal binding site is mutated in 3m1t.

    Ligand Summary




    No references found.

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