The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of putative NADPH-dependent oxidoreductase (ZP_01370612.1) from DESULFITOBACTERIUM HAFNIENSE DCB-2 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3db2 Target Id 379259
    Molecular Characteristics
    Source Desulfitobacterium hafniense dcb-2
    Alias Ids TPS7168,DHAF_12NOV03_CONTIG1044_REVISED_GENE999, 335482 Molecular Weight 39424.80 Da.
    Residues 353 Isoelectric Point 5.44
    Sequence mynpvgvaaiglgrwayvmadaytkseklklvtcysrtedkrekfgkryncagdatmeallaredvemv iitvpndkhaevieqcarsgkhiyvekpisvsldhaqridqviketgvkflcghssrrlgalrkmkemi dtkeigevssieavfsnerglelkkgnwrgepatapggpltqlgvhqidnlqfllgpvarvfnfgkpmy tevenitvnqtllefedgkqaylgtnwacpgvfsinvygtkanlfyqldfswwsnsdvtdehstlikre fasmsddpdnrilrdvkvdfesvdhlrveveevadvirnggeteigaeaslrnlavvlaavksvhekrp veiaeiig
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 1.70 Rfree 0.174
    Matthews' coefficent 2.29 Rfactor
    Waters 598 Solvent Content 46.23

    Ligand Information


    Google Scholar output for 3db2
    1. A novel _-N-acetylgalactosaminidase family with an NAD+-dependent catalytic mechanism suitable for enzymatic removal of blood group A antigens
    G Sulzenbacher, QP Liu, EP Bennett - Biocatalysis and , 2009 - informahealthcare.com
    2. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org

    Protein Summary

    The gene Dhaf_2064 from Desulfitobacterium hafniense dcb-2 encodes the YP_002458537 amino acid sequence with two domains: 1-120 belongs to the oxidoreductase family, NAD-binding Rossmann fold (PF01408); and 135-242  belongs to the oxidoreductase family, C-terminal alpha/beta domain (PF02894). SCOP classifies the N-terminal domain in the NADP-binding Rossmann fold superfamily and the C-terminal in the glyceraldehyde-3-phosphate dehydrogenase like C-terminal domain superfamily. YP_001273455, with 27% identical sequence, is annotated as a 3-chlorobenzoate-3,4-dioxygenase dyhydrogenase.

    3db2 structure is a a+b mixed protein with two beta sheets. There are three chains in the crystallographic asymmetric unit. However, the likely biological unit is a dimer (A+B and C+C association of the chains). According to DALI,  similar structures to 3db2 are: PDB:1evj (Z=36), PDB:1rye (Z=35), PDB:2glx (Z=38), 1h6a (Z=36) and JCSG structure PDB:1zh8 (Z=36, see topsan page) (Fig 3).

    FIg 1. 3db2 monomer architecture.

    Fig 2. The predicted biological unit is a dimer for 3db2.

    Fig 3. Similar structures (1evj 1rye 2glx 1h6a 1zh8) superimposed on 3db2 (in red).

    Ligand Summary




    No references found.

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