PDB entry 6ndg

View 6ndg on RCSB PDB site
Description: rhodocetin in complex with the integrin alpha2-a domain with yttrium bound
Class: cell adhesion/toxin
Keywords: C-TYPE LECTIN, INTEGRIN, VENOM, COAGULATION, CELL ADHESION, YTTRIUM, CELL ADHESION-TOXIN complex
Deposited on 2018-12-13, released 2019-01-23
The last revision prior to the SCOPe 2.07 freeze date was dated 2019-01-23, with a file datestamp of 2019-01-18.
Experiment type: XRAY
Resolution: 3.15 Å
R-factor: N/A
AEROSPACI score: 0.11 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Snaclec rhodocetin subunit gamma
    Species: Calloselasma rhodostoma [TaxId:8717]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndga_
  • Chain 'B':
    Compound: Snaclec rhodocetin subunit delta
    Species: Calloselasma rhodostoma [TaxId:8717]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgb_
  • Chain 'C':
    Compound: Integrin alpha-2
    Species: Homo sapiens [TaxId:9606]
    Gene: ITGA2, CD49B
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgc_
  • Chain 'D':
    Compound: Snaclec rhodocetin subunit gamma
    Species: Calloselasma rhodostoma [TaxId:8717]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgd_
  • Chain 'E':
    Compound: Snaclec rhodocetin subunit delta
    Species: Calloselasma rhodostoma [TaxId:8717]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndge_
  • Chain 'F':
    Compound: Integrin alpha-2
    Species: Homo sapiens [TaxId:9606]
    Gene: ITGA2, CD49B
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgf_
  • Chain 'G':
    Compound: Snaclec rhodocetin subunit gamma
    Species: Calloselasma rhodostoma [TaxId:8717]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgg_
  • Chain 'H':
    Compound: Snaclec rhodocetin subunit delta
    Species: Calloselasma rhodostoma [TaxId:8717]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgh_
  • Chain 'I':
    Compound: Integrin alpha-2
    Species: Homo sapiens [TaxId:9606]
    Gene: ITGA2, CD49B
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgi_
  • Chain 'J':
    Compound: Snaclec rhodocetin subunit gamma
    Species: Calloselasma rhodostoma [TaxId:8717]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgj_
  • Chain 'K':
    Compound: Snaclec rhodocetin subunit delta
    Species: Calloselasma rhodostoma [TaxId:8717]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgk_
  • Chain 'L':
    Compound: Integrin alpha-2
    Species: Homo sapiens [TaxId:9606]
    Gene: ITGA2, CD49B
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgl_
  • Chain 'M':
    Compound: Snaclec rhodocetin subunit gamma
    Species: Calloselasma rhodostoma [TaxId:8717]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgm_
  • Chain 'N':
    Compound: Snaclec rhodocetin subunit delta
    Species: Calloselasma rhodostoma [TaxId:8717]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgn_
  • Chain 'O':
    Compound: Integrin alpha-2
    Species: Homo sapiens [TaxId:9606]
    Gene: ITGA2, CD49B
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgo_
  • Chain 'P':
    Compound: Snaclec rhodocetin subunit gamma
    Species: Calloselasma rhodostoma [TaxId:8717]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgp_
  • Chain 'Q':
    Compound: Snaclec rhodocetin subunit delta
    Species: Calloselasma rhodostoma [TaxId:8717]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgq_
  • Chain 'R':
    Compound: Integrin alpha-2
    Species: Homo sapiens [TaxId:9606]
    Gene: ITGA2, CD49B
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6ndgr_
  • Heterogens: SO4, Y1, NA, CL, NH4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6ndgA (A:)
    dfnclpgwsaydqhcyqafnepktwdeaerfcteqakrghlvsigsdgeadfvaqlvtnn
    ikrpelyvwiglrdrrkeqqcssewsmsasiiyvnwntgesqmcqglarwtgfrkwdysd
    cqaknpfvckfpsec
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgA (A:)
    nclpgwsaydqhcyqafnepktwdeaerfcteqakrghlvsigsdgeadfvaqlvtnnik
    rpelyvwiglrdrrkeqqcssewsmsasiiyvnwntgesqmcqglarwtgfrkwdysdcq
    aknpfvckfps
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6ndgB (B:)
    cplhwssyngycyrvfselktwedaesfcyaqhkgsrlasihsreeeafvgklasqtlky
    tsmwlglnnpwkeckwewsddakldykvwlrrpycavmvvktdrifwfnrgcektvsfvc
    kfys
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgB (B:)
    cplhwssyngycyrvfselktwedaesfcyaqhkgsrlasihsreeeafvgklasqtlky
    tsmwlglnnpwkeckwewsddakldykvwlrrpycavmvvktdrifwfnrgcektvsfvc
    kf
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6ndgC (C:)
    mgsshhhhhhssglvprggspslidvvvvcdesnsiypwdavknflekfvqgldigptkt
    qvgliqyannprvvfnlntyktkeemivatsqtsqyggdltntfgaiqyarkyaysaasg
    grrsatkvmvvvtdgeshdgsmlkavidqcnhdnilrfgiavlgylnrnaldtknlikei
    kaiasipteryffnvsdeaallekagtlgeqifsieg
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgC (C:)
    lidvvvvcdesnsiypwdavknflekfvqgldigptktqvgliqyannprvvfnlntykt
    keemivatsqtsqyggdltntfgaiqyarkyaysaasggrrsatkvmvvvtdgeshdgsm
    lkavidqcnhdnilrfgiavlgylnrnaldtknlikeikaiasipteryffnvsdeaall
    ekagtlgeqif
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6ndgD (D:)
    dfnclpgwsaydqhcyqafnepktwdeaerfcteqakrghlvsigsdgeadfvaqlvtnn
    ikrpelyvwiglrdrrkeqqcssewsmsasiiyvnwntgesqmcqglarwtgfrkwdysd
    cqaknpfvckfpsec
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgD (D:)
    nclpgwsaydqhcyqafnepktwdeaerfcteqakrghlvsigsdgeadfvaqlvtnnik
    rpelyvwiglrdrrkeqqcssewsmsasiiyvnwntgesqmcqglarwtgfrkwdysdcq
    aknpfvckfps
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >6ndgE (E:)
    cplhwssyngycyrvfselktwedaesfcyaqhkgsrlasihsreeeafvgklasqtlky
    tsmwlglnnpwkeckwewsddakldykvwlrrpycavmvvktdrifwfnrgcektvsfvc
    kfys
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgE (E:)
    cplhwssyngycyrvfselktwedaesfcyaqhkgsrlasihsreeeafvgklasqtlky
    tsmwlglnnpwkeckwewsddakldykvwlrrpycavmvvktdrifwfnrgcektvsfvc
    kf
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >6ndgF (F:)
    mgsshhhhhhssglvprggspslidvvvvcdesnsiypwdavknflekfvqgldigptkt
    qvgliqyannprvvfnlntyktkeemivatsqtsqyggdltntfgaiqyarkyaysaasg
    grrsatkvmvvvtdgeshdgsmlkavidqcnhdnilrfgiavlgylnrnaldtknlikei
    kaiasipteryffnvsdeaallekagtlgeqifsieg
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgF (F:)
    lidvvvvcdesnsiypwdavknflekfvqgldigptktqvgliqyannprvvfnlntykt
    keemivatsqtsqyggdltntfgaiqyarkyaysaasggrrsatkvmvvvtdgeshdgsm
    lkavidqcnhdnilrfgiavlgylnrnaldtknlikeikaiasipteryffnvsdeaall
    ekagtlgeqif
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >6ndgG (G:)
    dfnclpgwsaydqhcyqafnepktwdeaerfcteqakrghlvsigsdgeadfvaqlvtnn
    ikrpelyvwiglrdrrkeqqcssewsmsasiiyvnwntgesqmcqglarwtgfrkwdysd
    cqaknpfvckfpsec
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgG (G:)
    nclpgwsaydqhcyqafnepktwdeaerfcteqakrghlvsigsdgeadfvaqlvtnnik
    rpelyvwiglrdrrkeqqcssewsmsasiiyvnwntgesqmcqglarwtgfrkwdysdcq
    aknpfvckfps
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >6ndgH (H:)
    cplhwssyngycyrvfselktwedaesfcyaqhkgsrlasihsreeeafvgklasqtlky
    tsmwlglnnpwkeckwewsddakldykvwlrrpycavmvvktdrifwfnrgcektvsfvc
    kfys
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgH (H:)
    cplhwssyngycyrvfselktwedaesfcyaqhkgsrlasihsreeeafvgklasqtlky
    tsmwlglnnpwkeckwewsddakldykvwlrrpycavmvvktdrifwfnrgcektvsfvc
    kf
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >6ndgI (I:)
    mgsshhhhhhssglvprggspslidvvvvcdesnsiypwdavknflekfvqgldigptkt
    qvgliqyannprvvfnlntyktkeemivatsqtsqyggdltntfgaiqyarkyaysaasg
    grrsatkvmvvvtdgeshdgsmlkavidqcnhdnilrfgiavlgylnrnaldtknlikei
    kaiasipteryffnvsdeaallekagtlgeqifsieg
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgI (I:)
    lidvvvvcdesnsiypwdavknflekfvqgldigptktqvgliqyannprvvfnlntykt
    keemivatsqtsqyggdltntfgaiqyarkyaysaasggrrsatkvmvvvtdgeshdgsm
    lkavidqcnhdnilrfgiavlgylnrnaldtknlikeikaiasipteryffnvsdeaall
    ekagtlgeqif
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >6ndgJ (J:)
    dfnclpgwsaydqhcyqafnepktwdeaerfcteqakrghlvsigsdgeadfvaqlvtnn
    ikrpelyvwiglrdrrkeqqcssewsmsasiiyvnwntgesqmcqglarwtgfrkwdysd
    cqaknpfvckfpsec
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgJ (J:)
    nclpgwsaydqhcyqafnepktwdeaerfcteqakrghlvsigsdgeadfvaqlvtnnik
    rpelyvwiglrdrrkeqqcssewsmsasiiyvnwntgesqmcqglarwtgfrkwdysdcq
    aknpfvckfps
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >6ndgK (K:)
    cplhwssyngycyrvfselktwedaesfcyaqhkgsrlasihsreeeafvgklasqtlky
    tsmwlglnnpwkeckwewsddakldykvwlrrpycavmvvktdrifwfnrgcektvsfvc
    kfys
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgK (K:)
    cplhwssyngycyrvfselktwedaesfcyaqhkgsrlasihsreeeafvgklasqtlky
    tsmwlglnnpwkeckwewsddakldykvwlrrpycavmvvktdrifwfnrgcektvsfvc
    kf
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >6ndgL (L:)
    mgsshhhhhhssglvprggspslidvvvvcdesnsiypwdavknflekfvqgldigptkt
    qvgliqyannprvvfnlntyktkeemivatsqtsqyggdltntfgaiqyarkyaysaasg
    grrsatkvmvvvtdgeshdgsmlkavidqcnhdnilrfgiavlgylnrnaldtknlikei
    kaiasipteryffnvsdeaallekagtlgeqifsieg
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgL (L:)
    lidvvvvcdesnsiypwdavknflekfvqgldigptktqvgliqyannprvvfnlntykt
    keemivatsqtsqyggdltntfgaiqyarkyaysaasggrrsatkvmvvvtdgeshdgsm
    lkavidqcnhdnilrfgiavlgylnrnaldtknlikeikaiasipteryffnvsdeaall
    ekagtlgeqif
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >6ndgM (M:)
    dfnclpgwsaydqhcyqafnepktwdeaerfcteqakrghlvsigsdgeadfvaqlvtnn
    ikrpelyvwiglrdrrkeqqcssewsmsasiiyvnwntgesqmcqglarwtgfrkwdysd
    cqaknpfvckfpsec
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgM (M:)
    nclpgwsaydqhcyqafnepktwdeaerfcteqakrghlvsigsdgeadfvaqlvtnnik
    rpelyvwiglrdrrkeqqcssewsmsasiiyvnwntgesqmcqglarwtgfrkwdysdcq
    aknpfvckfps
    

  • Chain 'N':
    Sequence, based on SEQRES records: (download)
    >6ndgN (N:)
    cplhwssyngycyrvfselktwedaesfcyaqhkgsrlasihsreeeafvgklasqtlky
    tsmwlglnnpwkeckwewsddakldykvwlrrpycavmvvktdrifwfnrgcektvsfvc
    kfys
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgN (N:)
    cplhwssyngycyrvfselktwedaesfcyaqhkgsrlasihsreeeafvgklasqtlky
    tsmwlglnnpwkeckwewsddakldykvwlrrpycavmvvktdrifwfnrgcektvsfvc
    kf
    

  • Chain 'O':
    Sequence, based on SEQRES records: (download)
    >6ndgO (O:)
    mgsshhhhhhssglvprggspslidvvvvcdesnsiypwdavknflekfvqgldigptkt
    qvgliqyannprvvfnlntyktkeemivatsqtsqyggdltntfgaiqyarkyaysaasg
    grrsatkvmvvvtdgeshdgsmlkavidqcnhdnilrfgiavlgylnrnaldtknlikei
    kaiasipteryffnvsdeaallekagtlgeqifsieg
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgO (O:)
    lidvvvvcdesnsiypwdavknflekfvqgldigptktqvgliqyannprvvfnlntykt
    keemivatsqtsqyggdltntfgaiqyarkyaysaasggrrsatkvmvvvtdgeshdgsm
    lkavidqcnhdnilrfgiavlgylnrnaldtknlikeikaiasipteryffnvsdeaall
    ekagtlgeqif
    

  • Chain 'P':
    Sequence, based on SEQRES records: (download)
    >6ndgP (P:)
    dfnclpgwsaydqhcyqafnepktwdeaerfcteqakrghlvsigsdgeadfvaqlvtnn
    ikrpelyvwiglrdrrkeqqcssewsmsasiiyvnwntgesqmcqglarwtgfrkwdysd
    cqaknpfvckfpsec
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgP (P:)
    nclpgwsaydqhcyqafnepktwdeaerfcteqakrghlvsigsdgeadfvaqlvtnnik
    rpelyvwiglrdrrkeqqcssewsmsasiiyvnwntgesqmcqglarwtgfrkwdysdcq
    aknpfvckfps
    

  • Chain 'Q':
    Sequence, based on SEQRES records: (download)
    >6ndgQ (Q:)
    cplhwssyngycyrvfselktwedaesfcyaqhkgsrlasihsreeeafvgklasqtlky
    tsmwlglnnpwkeckwewsddakldykvwlrrpycavmvvktdrifwfnrgcektvsfvc
    kfys
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgQ (Q:)
    cplhwssyngycyrvfselktwedaesfcyaqhkgsrlasihsreeeafvgklasqtlky
    tsmwlglnnpwkeckwewsddakldykvwlrrpycavmvvktdrifwfnrgcektvsfvc
    kf
    

  • Chain 'R':
    Sequence, based on SEQRES records: (download)
    >6ndgR (R:)
    mgsshhhhhhssglvprggspslidvvvvcdesnsiypwdavknflekfvqgldigptkt
    qvgliqyannprvvfnlntyktkeemivatsqtsqyggdltntfgaiqyarkyaysaasg
    grrsatkvmvvvtdgeshdgsmlkavidqcnhdnilrfgiavlgylnrnaldtknlikei
    kaiasipteryffnvsdeaallekagtlgeqifsieg
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ndgR (R:)
    lidvvvvcdesnsiypwdavknflekfvqgldigptktqvgliqyannprvvfnlntykt
    keemivatsqtsqyggdltntfgaiqyarkyaysaasggrrsatkvmvvvtdgeshdgsm
    lkavidqcnhdnilrfgiavlgylnrnaldtknlikeikaiasipteryffnvsdeaall
    ekagtlgeqif