PDB entry 3rit

View 3rit on RCSB PDB site
Description: Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg and dipeptide L-Arg-D-Lys
Class: isomerase
Keywords: TIM barrel, chloromuconate cycloisomerase, isomerase
Deposited on 2011-04-14, released 2011-04-27
The last revision prior to the SCOPe 2.03 freeze date was dated 2012-03-28, with a file datestamp of 2012-03-23.
Experiment type: XRAY
Resolution: 2.7 Å
R-factor: 0.177
AEROSPACI score: 0.31 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Dipeptide Epimerase
    Species: Methylococcus capsulatus [TaxId:414]
    Gene: MCA1834
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3rita1, d3rita2
  • Chain 'B':
    Compound: Dipeptide Epimerase
    Species: Methylococcus capsulatus [TaxId:414]
    Gene: MCA1834
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3ritb1, d3ritb2
  • Chain 'C':
    Compound: Dipeptide Epimerase
    Species: Methylococcus capsulatus [TaxId:414]
    Gene: MCA1834
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3ritc1, d3ritc2
  • Chain 'D':
    Compound: Dipeptide Epimerase
    Species: Methylococcus capsulatus [TaxId:414]
    Gene: MCA1834
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3ritd1, d3ritd2
  • Chain 'E':
    Compound: Dipeptide Epimerase
    Species: Methylococcus capsulatus [TaxId:414]
    Gene: MCA1834
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3rite1, d3rite2
  • Heterogens: SO4, ARG, DLY, MG, 1PE, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3ritA (A:)
    mkiadiqvrtehfpltrpyriafrsieeidnliveirtadgllglgaasperhvtgetle
    achaaldhdrlgwlmgrdirtlprlcrelaerlpaapaaraaldmalhdlvaqclglplv
    eilgrahdslptsvtigikpveetlaearehlalgfrvlkvklcgdeeqdferlrrlhet
    lagravvrvdpnqsydrdgllrldrlvqelgiefieqpfpagrtdwlralpkairrriaa
    desllgpadafalaappaacgifniklmkcgglaparriatiaetagidlmwgcmdesri
    siaaalhaalacpatryldldgsfdlardvaeggfiledgrlrvterpglglvypd
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ritA (A:)
    mkiadiqvrtehfpltrpyriafrsieeidnliveirtadgllglgaasperhvtgetle
    achaaldhdrlgwlmgrdirtlprlcrelaerlpaapaaraaldmalhdlvaqclglplv
    eilgrahdslptsvtigikpveetlaearehlalgfrvlkvklcgdeeqdferlrrlhet
    lagravvrvdpnqsydrdgllrldrlvqelgiefieqpfpagrtdwlralpkairrriaa
    desllgpadafalaappaacgifniklmkcgglaparriatiaetagidlmwgcmdesri
    siaaalhaalacpatryldldgsfdlardvaeggfiledgrlrvterpglglvy
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3ritB (B:)
    mkiadiqvrtehfpltrpyriafrsieeidnliveirtadgllglgaasperhvtgetle
    achaaldhdrlgwlmgrdirtlprlcrelaerlpaapaaraaldmalhdlvaqclglplv
    eilgrahdslptsvtigikpveetlaearehlalgfrvlkvklcgdeeqdferlrrlhet
    lagravvrvdpnqsydrdgllrldrlvqelgiefieqpfpagrtdwlralpkairrriaa
    desllgpadafalaappaacgifniklmkcgglaparriatiaetagidlmwgcmdesri
    siaaalhaalacpatryldldgsfdlardvaeggfiledgrlrvterpglglvypd
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ritB (B:)
    mkiadiqvrtehfpltrpyriafrsieeidnliveirtadgllglgaasperhvtgetle
    achaaldhdrlgwlmgrdirtlprlcrelaerlpaapaaraaldmalhdlvaqclglplv
    eilgrahdslptsvtigikpveetlaearehlalgfrvlkvklcgdeeqdferlrrlhet
    lagravvrvdpnqsydrdgllrldrlvqelgiefieqpfpagrtdwlralpkairrriaa
    desllgpadafalaappaacgifniklmkcgglaparriatiaetagidlmwgcmdesri
    siaaalhaalacpatryldldgsfdlardvaeggfiledgrlrvterpglglvy
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3ritC (C:)
    mkiadiqvrtehfpltrpyriafrsieeidnliveirtadgllglgaasperhvtgetle
    achaaldhdrlgwlmgrdirtlprlcrelaerlpaapaaraaldmalhdlvaqclglplv
    eilgrahdslptsvtigikpveetlaearehlalgfrvlkvklcgdeeqdferlrrlhet
    lagravvrvdpnqsydrdgllrldrlvqelgiefieqpfpagrtdwlralpkairrriaa
    desllgpadafalaappaacgifniklmkcgglaparriatiaetagidlmwgcmdesri
    siaaalhaalacpatryldldgsfdlardvaeggfiledgrlrvterpglglvypd
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ritC (C:)
    mkiadiqvrtehfpltrpyriafrsieeidnliveirtadgllglgaasperhvtgetle
    achaaldhdrlgwlmgrdirtlprlcrelaerlpaapaaraaldmalhdlvaqclglplv
    eilgrahdslptsvtigikpveetlaearehlalgfrvlkvklcgdeeqdferlrrlhet
    lagravvrvdpnqsydrdgllrldrlvqelgiefieqpfpagrtdwlralpkairrriaa
    desllgpadafalaappaacgifniklmkcgglaparriatiaetagidlmwgcmdesri
    siaaalhaalacpatryldldgsfdlardvaeggfiledgrlrvterpglglvy
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3ritD (D:)
    mkiadiqvrtehfpltrpyriafrsieeidnliveirtadgllglgaasperhvtgetle
    achaaldhdrlgwlmgrdirtlprlcrelaerlpaapaaraaldmalhdlvaqclglplv
    eilgrahdslptsvtigikpveetlaearehlalgfrvlkvklcgdeeqdferlrrlhet
    lagravvrvdpnqsydrdgllrldrlvqelgiefieqpfpagrtdwlralpkairrriaa
    desllgpadafalaappaacgifniklmkcgglaparriatiaetagidlmwgcmdesri
    siaaalhaalacpatryldldgsfdlardvaeggfiledgrlrvterpglglvypd
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ritD (D:)
    mkiadiqvrtehfpltrpyriafrsieeidnliveirtadgllglgaasperhvtgetle
    achaaldhdrlgwlmgrdirtlprlcrelaerlpaapaaraaldmalhdlvaqclglplv
    eilgrahdslptsvtigikpveetlaearehlalgfrvlkvklcgdeeqdferlrrlhet
    lagravvrvdpnqsydrdgllrldrlvqelgiefieqpfpagrtdwlralpkairrriaa
    desllgpadafalaappaacgifniklmkcgglaparriatiaetagidlmwgcmdesri
    siaaalhaalacpatryldldgsfdlardvaeggfiledgrlrvterpglglvy
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3ritE (E:)
    mkiadiqvrtehfpltrpyriafrsieeidnliveirtadgllglgaasperhvtgetle
    achaaldhdrlgwlmgrdirtlprlcrelaerlpaapaaraaldmalhdlvaqclglplv
    eilgrahdslptsvtigikpveetlaearehlalgfrvlkvklcgdeeqdferlrrlhet
    lagravvrvdpnqsydrdgllrldrlvqelgiefieqpfpagrtdwlralpkairrriaa
    desllgpadafalaappaacgifniklmkcgglaparriatiaetagidlmwgcmdesri
    siaaalhaalacpatryldldgsfdlardvaeggfiledgrlrvterpglglvypd
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ritE (E:)
    mkiadiqvrtehfpltrpyriafrsieeidnliveirtadgllglgaasperhvtgetle
    achaaldhdrlgwlmgrdirtlprlcrelaerlpaapaaraaldmalhdlvaqclglplv
    eilgrahdslptsvtigikpveetlaearehlalgfrvlkvklcgdeeqdferlrrlhet
    lagravvrvdpnqsydrdgllrldrlvqelgiefieqpfpagrtdwlralpkairrriaa
    desllgpadafalaappaacgifniklmkcgglaparriatiaetagidlmwgcmdesri
    siaaalhaalacpatryldldgsfdlardvaeggfiledgrlrvterpglglvy