PDB entry 3vpf

View 3vpf on RCSB PDB site
Description: Complex structure of Lactobacillus casei lactate dehydrogenase penta mutant with pyruvate
Class: oxidoreductase
Keywords: Rossmann Fold, Dehydrogenase, NADH Binding, OXIDOREDUCTASE
Deposited on 2012-03-01, released 2013-03-06
Made obsolete by 6j9u on 2019-02-06

The last revision prior to the SCOPe 2.06 freeze date was dated 2013-03-06, with a file datestamp of 2013-03-01.
Experiment type: XRAY
Resolution: 2.79 Å
R-factor: 0.186
AEROSPACI score: 0.26 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: l-lactate dehydrogenase
    Species: Lactobacillus casei [TaxId:1582]
    Gene: LDH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00343
      • engineered mutation (54-55)
      • engineered mutation (163)
      • engineered mutation (222-223)
    Domains in SCOPe 2.06: d3vpfa1, d3vpfa2
  • Chain 'B':
    Compound: l-lactate dehydrogenase
    Species: Lactobacillus casei [TaxId:1582]
    Gene: LDH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00343
      • engineered mutation (54-55)
      • engineered mutation (163)
      • engineered mutation (222-223)
    Domains in SCOPe 2.06: d3vpfb1, d3vpfb2
  • Chain 'C':
    Compound: l-lactate dehydrogenase
    Species: Lactobacillus casei [TaxId:1582]
    Gene: LDH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00343
      • engineered mutation (54-55)
      • engineered mutation (163)
      • engineered mutation (222-223)
    Domains in SCOPe 2.06: d3vpfc1, d3vpfc2
  • Chain 'D':
    Compound: l-lactate dehydrogenase
    Species: Lactobacillus casei [TaxId:1582]
    Gene: LDH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00343
      • engineered mutation (54-55)
      • engineered mutation (163)
      • engineered mutation (222-223)
    Domains in SCOPe 2.06: d3vpfd1, d3vpfd2
  • Chain 'E':
    Compound: l-lactate dehydrogenase
    Species: Lactobacillus casei [TaxId:1582]
    Gene: LDH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00343
      • engineered mutation (54-55)
      • engineered mutation (163)
      • engineered mutation (222-223)
    Domains in SCOPe 2.06: d3vpfe1, d3vpfe2
  • Chain 'F':
    Compound: l-lactate dehydrogenase
    Species: Lactobacillus casei [TaxId:1582]
    Gene: LDH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00343
      • engineered mutation (54-55)
      • engineered mutation (163)
      • engineered mutation (222-223)
    Domains in SCOPe 2.06: d3vpff1, d3vpff2
  • Heterogens: PYR, SO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3vpfA (A:)
    masitdkdhqkvilvgdgavgssyayamvlqgiaqeigivdifkdktkgdaidledalpf
    tspkkiysaeysdakdadlvvitagapqkpgetrldlvnknlkilksivdpivdsgfngi
    flvaanpvdiltyatwklsgfpknrvvgsgtsldtarfrqsiakmvnvdarsvhayimge
    hgdtefpvwshaniggvtiaewvkahpeikedklvkmfedvrnkayeiiklkgatfygia
    talariskailndenavlplsvymdgqyglndiyigtpavinrngiqnileipltdheee
    smqksasqlkkvltdafakndietrq
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vpfA (A:)
    itdkdhqkvilvgdgavgssyayamvlqgiaqeigivdifkdktkgdaidledalpftsp
    kkiysaeysdakdadlvvitagaptrldlvnknlkilksivdpivdsgfngiflvaanpv
    diltyatwklsgfpknrvvgsgtsldtarfrqsiakmvnvdarsvhayimgehgdtefpv
    wshaniggvtiaewvkahpeikedklvkmfedvrnkayeiiklkgatfygiatalarisk
    ailndenavlplsvymdgqyglndiyigtpavinrngiqnileipltdheeesmqksasq
    lkkvlt
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3vpfB (B:)
    masitdkdhqkvilvgdgavgssyayamvlqgiaqeigivdifkdktkgdaidledalpf
    tspkkiysaeysdakdadlvvitagapqkpgetrldlvnknlkilksivdpivdsgfngi
    flvaanpvdiltyatwklsgfpknrvvgsgtsldtarfrqsiakmvnvdarsvhayimge
    hgdtefpvwshaniggvtiaewvkahpeikedklvkmfedvrnkayeiiklkgatfygia
    talariskailndenavlplsvymdgqyglndiyigtpavinrngiqnileipltdheee
    smqksasqlkkvltdafakndietrq
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vpfB (B:)
    itdkdhqkvilvgdgavgssyayamvlqgiaqeigivdifkdktkgdaidledalpftsp
    kkiysaeysdakdadlvvitagapqkpgetrldlvnknlkilksivdpivdsgfngiflv
    aanpvdiltyatwklsgfpknrvvgsgtsldtarfrqsiakmvnvdarsvhayimgehgd
    tefpvwshaniggvtiaewvkahpeikedklvkmfedvrnkayeiiklkgatfygiatal
    ariskailndenavlplsvymdgqyglndiyigtpavinrngiqnileipltdheeesmq
    ksasqlkkvltdaf
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3vpfC (C:)
    masitdkdhqkvilvgdgavgssyayamvlqgiaqeigivdifkdktkgdaidledalpf
    tspkkiysaeysdakdadlvvitagapqkpgetrldlvnknlkilksivdpivdsgfngi
    flvaanpvdiltyatwklsgfpknrvvgsgtsldtarfrqsiakmvnvdarsvhayimge
    hgdtefpvwshaniggvtiaewvkahpeikedklvkmfedvrnkayeiiklkgatfygia
    talariskailndenavlplsvymdgqyglndiyigtpavinrngiqnileipltdheee
    smqksasqlkkvltdafakndietrq
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vpfC (C:)
    sitdkdhqkvilvgdgavgssyayamvlqgiaqeigivdifkdktkgdaidledalpfts
    pkkiysaeysdakdadlvvitagapqkpgetrldlvnknlkilksivdpivdsgfngifl
    vaanpvdiltyatwklsgfpknrvvgsgtsldtarfrqsiakmvnvdarsvhayimgehg
    dtefpvwshaniggvtiaewvkahpeikedklvkmfedvrnkayeiiklkgatfygiata
    lariskailndenavlplsvymdgqyglndiyigtpavinrngiqnileipltdheeesm
    qksasqlkkvltdaf
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3vpfD (D:)
    masitdkdhqkvilvgdgavgssyayamvlqgiaqeigivdifkdktkgdaidledalpf
    tspkkiysaeysdakdadlvvitagapqkpgetrldlvnknlkilksivdpivdsgfngi
    flvaanpvdiltyatwklsgfpknrvvgsgtsldtarfrqsiakmvnvdarsvhayimge
    hgdtefpvwshaniggvtiaewvkahpeikedklvkmfedvrnkayeiiklkgatfygia
    talariskailndenavlplsvymdgqyglndiyigtpavinrngiqnileipltdheee
    smqksasqlkkvltdafakndietrq
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vpfD (D:)
    sitdkdhqkvilvgdgavgssyayamvlqgiaqeigivdifkdktkgdaidledalpfts
    pkkiysaeysdakdadlvvitagapqkpgetrldlvnknlkilksivdpivdsgfngifl
    vaanpvdiltyatwklsgfpknrvvgsgtsldtarfrqsiakmvnvdarsvhayimgehg
    dtefpvwshaniggvtiaewvkahpeikedklvkmfedvrnkayeiiklkgatfygiata
    lariskailndenavlplsvymdgqyglndiyigtpavinrngiqnileipltdheeesm
    qksasqlkkvltdaf
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3vpfE (E:)
    masitdkdhqkvilvgdgavgssyayamvlqgiaqeigivdifkdktkgdaidledalpf
    tspkkiysaeysdakdadlvvitagapqkpgetrldlvnknlkilksivdpivdsgfngi
    flvaanpvdiltyatwklsgfpknrvvgsgtsldtarfrqsiakmvnvdarsvhayimge
    hgdtefpvwshaniggvtiaewvkahpeikedklvkmfedvrnkayeiiklkgatfygia
    talariskailndenavlplsvymdgqyglndiyigtpavinrngiqnileipltdheee
    smqksasqlkkvltdafakndietrq
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vpfE (E:)
    tdkdhqkvilvgdgavgssyayamvlqgiaqeigivdifkdktkgdaidledalpftspk
    kiysaeysdakdadlvvitagapqkpgetrldlvnknlkilksivdpivdsgfngiflva
    anpvdiltyatwklsgfpknrvvgsgtsldtarfrqsiakmvnvdarsvhayimgehgdt
    efpvwshaniggvtiaewvkahpeikedklvkmfedvrnkayeiiklkgatfygiatala
    riskailndenavlplsvymdgqyglndiyigtpavinrngiqnileipltdheeesmqk
    sasqlkkvltdafa
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3vpfF (F:)
    masitdkdhqkvilvgdgavgssyayamvlqgiaqeigivdifkdktkgdaidledalpf
    tspkkiysaeysdakdadlvvitagapqkpgetrldlvnknlkilksivdpivdsgfngi
    flvaanpvdiltyatwklsgfpknrvvgsgtsldtarfrqsiakmvnvdarsvhayimge
    hgdtefpvwshaniggvtiaewvkahpeikedklvkmfedvrnkayeiiklkgatfygia
    talariskailndenavlplsvymdgqyglndiyigtpavinrngiqnileipltdheee
    smqksasqlkkvltdafakndietrq
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vpfF (F:)
    sitdkdhqkvilvgdgavgssyayamvlqgiaqeigivdifkdktkgdaidledalpfts
    pkkiysaeysdakdadlvvitagapqkpgetrldlvnknlkilksivdpivdsgfngifl
    vaanpvdiltyatwklsgfpknrvvgsgtsldtarfrqsiakmvnvdarsvhayimgehg
    dtefpvwshaniggvtiaewvkahpeikedklvkmfedvrnkayeiiklkgatfygiata
    lariskailndenavlplsvymdgqyglndiyigtpavinrngiqnileipltdheeesm
    qksasqlkkvltdafa