PDB entry 6c4c

View 6c4c on RCSB PDB site
Description: Crystal structure of 3-nitropropionate modified isocitrate lyase from Mycobacterium tuberculosis with glyoxylate and pyruvate
Class: lyase
Keywords: lyase
Deposited on 2018-01-11, released 2018-06-06
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-06-06, with a file datestamp of 2018-06-01.
Experiment type: XRAY
Resolution: 2.2 Å
R-factor: N/A
AEROSPACI score: 0.27 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Isocitrate lyase 1
    Species: Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) [TaxId:652616]
    Gene: icl1, ERDMAN_0512, Q643_00485
    Database cross-references and differences (RAF-indexed):
    • Uniprot H8EVV4 (14-End)
      • expression tag (13)
    Domains in SCOPe 2.07: d6c4ca1, d6c4ca2
  • Chain 'B':
    Compound: Isocitrate lyase 1
    Species: Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) [TaxId:652616]
    Gene: icl1, ERDMAN_0512, Q643_00485
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6c4cb_
  • Chain 'C':
    Compound: Isocitrate lyase 1
    Species: Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) [TaxId:652616]
    Gene: icl1, ERDMAN_0512, Q643_00485
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6c4cc_
  • Chain 'D':
    Compound: Isocitrate lyase 1
    Species: Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) [TaxId:652616]
    Gene: icl1, ERDMAN_0512, Q643_00485
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6c4cd_
  • Chain 'E':
    Compound: Isocitrate lyase 1
    Species: Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) [TaxId:652616]
    Gene: icl1, ERDMAN_0512, Q643_00485
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6c4ce_
  • Chain 'F':
    Compound: Isocitrate lyase 1
    Species: Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) [TaxId:652616]
    Gene: icl1, ERDMAN_0512, Q643_00485
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6c4cf_
  • Chain 'G':
    Compound: Isocitrate lyase 1
    Species: Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) [TaxId:652616]
    Gene: icl1, ERDMAN_0512, Q643_00485
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6c4cg_
  • Chain 'H':
    Compound: Isocitrate lyase 1
    Species: Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) [TaxId:652616]
    Gene: icl1, ERDMAN_0512, Q643_00485
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6c4ch_
  • Heterogens: GLV, MG, PYR, 3NP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6c4cA (A:)
    mhhhhhhlvprgshmsvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveeh
    tlarrgaevlweqlhdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghty
    pdqslypansvpqvvrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvye
    lqkaliaagvagshwedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvvi
    artdaeaatlitsdvderdqpfitgertregfyrtkngiepciarakayapfadliwmet
    gtpdleaarqfseavkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfi
    tlagfhalnysmfdlaygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdria
    ttvdpnssttaltgsteegqfh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6c4cA (A:)
    hmsvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveehtlarrgaevlweq
    lhdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghtypdqslypansvpq
    vvrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvyelqkaliaagvags
    hwedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvviartdaeaatlits
    dvderdqpfitgertregfyrtkngiepciarakayapfadliwmetgtpdleaarqfse
    avkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfitlagfhalnysmf
    dlaygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdriattvdpnssttalt
    gsteegqf
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6c4cB (B:)
    mhhhhhhlvprgshmsvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveeh
    tlarrgaevlweqlhdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghty
    pdqslypansvpqvvrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvye
    lqkaliaagvagshwedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvvi
    artdaeaatlitsdvderdqpfitgertregfyrtkngiepciarakayapfadliwmet
    gtpdleaarqfseavkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfi
    tlagfhalnysmfdlaygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdria
    ttvdpnssttaltgsteegqfh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6c4cB (B:)
    msvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveehtlarrgaevlweql
    hdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghtypdqslypansvpqv
    vrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvyelqkaliaagvagsh
    wedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvviartdaeaatlitsd
    vderdqpfitgertregfyrtkngiepciarakayapfadliwmetgtpdleaarqfsea
    vkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfitlagfhalnysmfd
    laygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdriattvdpnssttaltg
    steegqf
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6c4cC (C:)
    mhhhhhhlvprgshmsvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveeh
    tlarrgaevlweqlhdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghty
    pdqslypansvpqvvrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvye
    lqkaliaagvagshwedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvvi
    artdaeaatlitsdvderdqpfitgertregfyrtkngiepciarakayapfadliwmet
    gtpdleaarqfseavkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfi
    tlagfhalnysmfdlaygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdria
    ttvdpnssttaltgsteegqfh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6c4cC (C:)
    msvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveehtlarrgaevlweql
    hdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghtypdqslypansvpqv
    vrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvyelqkaliaagvagsh
    wedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvviartdaeaatlitsd
    vderdqpfitgertregfyrtkngiepciarakayapfadliwmetgtpdleaarqfsea
    vkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfitlagfhalnysmfd
    laygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdriattvdpnssttaltg
    steegqf
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6c4cD (D:)
    mhhhhhhlvprgshmsvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveeh
    tlarrgaevlweqlhdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghty
    pdqslypansvpqvvrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvye
    lqkaliaagvagshwedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvvi
    artdaeaatlitsdvderdqpfitgertregfyrtkngiepciarakayapfadliwmet
    gtpdleaarqfseavkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfi
    tlagfhalnysmfdlaygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdria
    ttvdpnssttaltgsteegqfh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6c4cD (D:)
    msvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveehtlarrgaevlweql
    hdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghtypdqslypansvpqv
    vrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvyelqkaliaagvagsh
    wedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvviartdaeaatlitsd
    vderdqpfitgertregfyrtkngiepciarakayapfadliwmetgtpdleaarqfsea
    vkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfitlagfhalnysmfd
    laygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdriattvdpnssttaltg
    steegqfh
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >6c4cE (E:)
    mhhhhhhlvprgshmsvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveeh
    tlarrgaevlweqlhdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghty
    pdqslypansvpqvvrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvye
    lqkaliaagvagshwedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvvi
    artdaeaatlitsdvderdqpfitgertregfyrtkngiepciarakayapfadliwmet
    gtpdleaarqfseavkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfi
    tlagfhalnysmfdlaygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdria
    ttvdpnssttaltgsteegqfh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6c4cE (E:)
    msvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveehtlarrgaevlweql
    hdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghtypdqslypansvpqv
    vrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvyelqkaliaagvagsh
    wedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvviartdaeaatlitsd
    vderdqpfitgertregfyrtkngiepciarakayapfadliwmetgtpdleaarqfsea
    vkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfitlagfhalnysmfd
    laygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdriattvdpnssttaltg
    steegqfh
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >6c4cF (F:)
    mhhhhhhlvprgshmsvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveeh
    tlarrgaevlweqlhdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghty
    pdqslypansvpqvvrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvye
    lqkaliaagvagshwedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvvi
    artdaeaatlitsdvderdqpfitgertregfyrtkngiepciarakayapfadliwmet
    gtpdleaarqfseavkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfi
    tlagfhalnysmfdlaygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdria
    ttvdpnssttaltgsteegqfh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6c4cF (F:)
    msvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveehtlarrgaevlweql
    hdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghtypdqslypansvpqv
    vrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvyelqkaliaagvagsh
    wedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvviartdaeaatlitsd
    vderdqpfitgertregfyrtkngiepciarakayapfadliwmetgtpdleaarqfsea
    vkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfitlagfhalnysmfd
    laygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdriattvdpnssttaltg
    steegqfh
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >6c4cG (G:)
    mhhhhhhlvprgshmsvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveeh
    tlarrgaevlweqlhdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghty
    pdqslypansvpqvvrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvye
    lqkaliaagvagshwedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvvi
    artdaeaatlitsdvderdqpfitgertregfyrtkngiepciarakayapfadliwmet
    gtpdleaarqfseavkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfi
    tlagfhalnysmfdlaygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdria
    ttvdpnssttaltgsteegqfh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6c4cG (G:)
    msvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveehtlarrgaevlweql
    hdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghtypdqslypansvpqv
    vrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvyelqkaliaagvagsh
    wedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvviartdaeaatlitsd
    vderdqpfitgertregfyrtkngiepciarakayapfadliwmetgtpdleaarqfsea
    vkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfitlagfhalnysmfd
    laygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdriattvdpnssttaltg
    steegqf
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >6c4cH (H:)
    mhhhhhhlvprgshmsvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveeh
    tlarrgaevlweqlhdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghty
    pdqslypansvpqvvrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvye
    lqkaliaagvagshwedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvvi
    artdaeaatlitsdvderdqpfitgertregfyrtkngiepciarakayapfadliwmet
    gtpdleaarqfseavkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfi
    tlagfhalnysmfdlaygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdria
    ttvdpnssttaltgsteegqfh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6c4cH (H:)
    msvvgtpksaeqiqqewdtnprwkdvtrtysaedvvalqgsvveehtlarrgaevlweql
    hdlewvnalgaltgnmavqqvraglkaiylsgwqvagdanlsghtypdqslypansvpqv
    vrrinnalqradqiakiegdtsvenwlapivadgeagfggalnvyelqkaliaagvagsh
    wedqlasekkxghlggkvliptqqhirtltsarlaadvadvptvviartdaeaatlitsd
    vderdqpfitgertregfyrtkngiepciarakayapfadliwmetgtpdleaarqfsea
    vkaeypdqmlayncspsfnwkkhlddatiakfqkelaamgfkfqfitlagfhalnysmfd
    laygyaqnqmsayvelqerefaaeergytatkhqrevgagyfdriattvdpnssttaltg
    steegqfh