PDB entry 2vmf

View 2vmf on RCSB PDB site
Description: structural and biochemical evidence for a boat-like transition state in beta-mannosidases
Class: hydrolase
Keywords: linear free energy relationship, transition state mimic, mannosidase, glycoside hydrolase, hydrolase
Deposited on 2008-01-25, released 2008-04-01
The last revision prior to the SCOPe 2.03 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.1 Å
R-factor: 0.167
AEROSPACI score: 0.45 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: beta-mannosidase
    Species: BACTEROIDES THETAIOTAOMICRON [TaxId:226186]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8AAK6 (Start-838)
    • PDB 2VMF
    Domains in SCOPe 2.03: d2vmfa1, d2vmfa2, d2vmfa3, d2vmfa4, d2vmfa5
  • Chain 'B':
    Compound: beta-mannosidase
    Species: BACTEROIDES THETAIOTAOMICRON [TaxId:226186]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8AAK6 (Start-838)
    • PDB 2VMF (839-End)
    Domains in SCOPe 2.03: d2vmfb1, d2vmfb2, d2vmfb3, d2vmfb4, d2vmfb5
  • Heterogens: MVL, EDO, BR, CL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2vmfA (A:)
    qgndtsevmlldtgwefsqsgtekwmpatvpgtvhqdlishellpnpfygmnekkiqwve
    nedweyrtsfivseeqlnrdgiqlifegldtyadvylngslllkadnmfvgytlpvksvl
    rkgenhlyiyfhspirqtlpqyasngfnypadndhhekhlsvfsrkapysygwdwgirmv
    tsgvwrpvtlrfydiatisdyyvrqlsltdenarlsnelivnqivpqkipaevrvnvsln
    gttvtevkqqvtlqpginhitlpaevtnpvrwmpngwgtptlydfsaqiacgdrivaeqs
    hriglrtirvvnekdkdgesfyfevngipmfakganyipqdallpnvtteryqtlfrdmk
    eanmnmvriwgggtyennlfydladengilvwqdfmfactpypsdptflkrveaeavyni
    rrlrnhaslamwcgnneilealkywgfekkftpevyqglmhgydklfrellpstvkefds
    drfyvhsspylanwgrpeswgtgdshnwgvwygkkpfesldtdlprfmsefgfqsfpemk
    tiaafaapedyqiesevmnahqkssignslirtymerdyiipesfedfvyvglvlqgqgm
    rhgleahrrnrpycmgtlywqlndswpvvswssidyygnwkalhyqakrafapvlinpiq
    qndslsvylisdrldtmeqmtlemkvvdfdgktlgkkiqvhslevpantskcvyrakldg
    wltpedcrrsflklilkdksghqvaesvhffrktkdlqlpptsvsyqmkqtdgkceltlf
    ssmlakdifietplqgarysdnffdllpgerkkviitsprikkgeelpvnikhiretyke
    hhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vmfA (A:)
    ndtsevmlldtgwefsqsgtekwmpatvpgtvhqdlishellpnpfygmnekkiqwvene
    dweyrtsfivseeqlnrdgiqlifegldtyadvylngslllkadnmfvgytlpvksvlrk
    genhlyiyfhspirqtlpqyasngfnypadndhhekhlsvfsrkapysygwdwgirmvts
    gvwrpvtlrfydiatisdyyvrqlsltdenarlsnelivnqivpqkipaevrvnvslngt
    tvtevkqqvtlqpginhitlpaevtnpvrwmpngwgtptlydfsaqiacgrivaeqshri
    glrtirvvnekdkdgesfyfevngipmfakganyipqdallpnvtteryqtlfrdmkean
    mnmvriwgggtyennlfydladengilvwqdfmfactpypsdptflkrveaeavynirrl
    rnhaslamwcgnneilealkywgfekkftpevyqglmhgydklfrellpstvkefdsdrf
    yvhsspylanwgrpeswgtgdshnwgvwygkkpfesldtdlprfmsefgfqsfpemktia
    afaapedyqiesevmnahqkssignslirtymerdyiipesfedfvyvglvlqgqgmrhg
    leahrrnrpycmgtlywqlndswpvvswssidyygnwkalhyqakrafapvlinpiqqnd
    slsvylisdrldtmeqmtlemkvvdfdgktlgkkiqvhslevpantskcvyrakldgwlt
    pedcrrsflklilkdksghqvaesvhffrktkdlqlpptsvsyqmkqtdgkceltlfssm
    lakdifietplqgarysdnffdllpgerkkviitsprikkgelpvnikhiretyk
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2vmfB (B:)
    qgndtsevmlldtgwefsqsgtekwmpatvpgtvhqdlishellpnpfygmnekkiqwve
    nedweyrtsfivseeqlnrdgiqlifegldtyadvylngslllkadnmfvgytlpvksvl
    rkgenhlyiyfhspirqtlpqyasngfnypadndhhekhlsvfsrkapysygwdwgirmv
    tsgvwrpvtlrfydiatisdyyvrqlsltdenarlsnelivnqivpqkipaevrvnvsln
    gttvtevkqqvtlqpginhitlpaevtnpvrwmpngwgtptlydfsaqiacgdrivaeqs
    hriglrtirvvnekdkdgesfyfevngipmfakganyipqdallpnvtteryqtlfrdmk
    eanmnmvriwgggtyennlfydladengilvwqdfmfactpypsdptflkrveaeavyni
    rrlrnhaslamwcgnneilealkywgfekkftpevyqglmhgydklfrellpstvkefds
    drfyvhsspylanwgrpeswgtgdshnwgvwygkkpfesldtdlprfmsefgfqsfpemk
    tiaafaapedyqiesevmnahqkssignslirtymerdyiipesfedfvyvglvlqgqgm
    rhgleahrrnrpycmgtlywqlndswpvvswssidyygnwkalhyqakrafapvlinpiq
    qndslsvylisdrldtmeqmtlemkvvdfdgktlgkkiqvhslevpantskcvyrakldg
    wltpedcrrsflklilkdksghqvaesvhffrktkdlqlpptsvsyqmkqtdgkceltlf
    ssmlakdifietplqgarysdnffdllpgerkkviitsprikkgeelpvnikhiretyke
    hhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vmfB (B:)
    gndtsevmlldtgwefsqsgtekwmpatvpgtvhqdlishellpnpfygmnekkiqwven
    edweyrtsfivseeqlnrdgiqlifegldtyadvylngslllkadnmfvgytlpvksvlr
    kgenhlyiyfhspirqtlpqyasngfnypadndhhekhlsvfsrkapysygwdwgirmvt
    sgvwrpvtlrfydiatisdyyvrqlsltdenarlsnelivnqivpqkipaevrvnvslng
    ttvtevkqqvtlqpginhitlpaevtnpvrwmpngwgtptlydfsaqiacgdrivaeqsh
    riglrtirvvnekdkdgesfyfevngipmfakganyipqdallpnvtteryqtlfrdmke
    anmnmvriwgggtyennlfydladengilvwqdfmfactpypsdptflkrveaeavynir
    rlrnhaslamwcgnneilealkywgfekkftpevyqglmhgydklfrellpstvkefdsd
    rfyvhsspylanwgrpeswgtgdshnwgvwygkkpfesldtdlprfmsefgfqsfpemkt
    iaafaapedyqiesevmnahqkssignslirtymerdyiipesfedfvyvglvlqgqgmr
    hgleahrrnrpycmgtlywqlndswpvvswssidyygnwkalhyqakrafapvlinpiqq
    ndslsvylisdrldtmeqmtlemkvvdfdgktlgkkiqvhslevpantskcvyrakldgw
    ltpedcrrsflklilkdsghqvaesvhffrktkdlqlpptsvsyqmkqtdgkceltlfss
    mlakdifietplqgarysdnffdllpgerkkviitsprikkgeelpvnikhiretykehh