PDB entry 5ijd

View 5ijd on RCSB PDB site
Description: the crystal structure of mouse tlr4/md-2/lipid a complex
Deposited on 2016-03-01, released 2016-04-27
The last revision was dated 2020-07-29, with a file datestamp of 2020-07-04.
Experiment type: XRAY
Resolution: 2.7 Å
R-factor: N/A
AEROSPACI score: 0.16 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Toll-like receptor 4, Variable lymphocyte receptor B chimera
    Species: Eptatretus burgeri [TaxId:7764]
    Gene: VLRB
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: Toll-like receptor 4, Variable lymphocyte receptor B chimera
    Species: Eptatretus burgeri [TaxId:7764]
    Gene: VLRB
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Lymphocyte antigen 96
    Species: Mus musculus [TaxId:10090]
    Gene: LY96, ESOP1, MD2
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: Lymphocyte antigen 96
    Species: Mus musculus [TaxId:10090]
    Gene: LY96, ESOP1, MD2
    Database cross-references and differences (RAF-indexed):
  • Heterogens: NAG, LP4, LP5, DAO, MYR, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.07, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >5ijdA (A:)
    npcievvpnityqcmdqklskvpddipsstknidlsfnplkilksysfsnfselqwldls
    rceietiedkawhglhhlsnliltgnpiqsfspgsfsgltslenlvavetklaslesfpi
    gqlitlkklnvahnfihscklpayfsnltnlvhvdlsynyiqtitvndlqflrenpqvnl
    sldmslnpidfiqdqafqgiklheltlrgnfnssnimktclqnlaglhvhrlilgefkde
    rnleifepsimeglcdvtidefrltytndfsddivkfhclanvsamslagvsikyledvp
    khfkwqslsiircqlkqfptldlpflksltltmnkgsisfkkvalpslsyldlsrnalsf
    sgccsysdlgtnslrhldlsfngaiimsanfmgleelqhldfqhstlkrvtefsaflsle
    kllyldisytntkidfdgiflgltslntlkmagnsfkdntlsnvfanttnltfldlskcq
    leqiswgvfdtlhrlqllnmshnnllfldsshynqlyslkelaldtnqlksvpdgifdrl
    tslqkiwlhtnpwdcscpridylsrwlnknsqkeqgsakcsgsgkpvrsiicpt
    

    Sequence, based on observed residues (ATOM records):
    >5ijdA (A:)
    ievvpnityqcmdqklskvpddipsstknidlsfnplkilksysfsnfselqwldlsrce
    ietiedkawhglhhlsnliltgnpiqsfspgsfsgltslenlvavetklaslesfpigql
    itlkklnvahnfihscklpayfsnltnlvhvdlsynyiqtitvndlqflrenpqvnlsld
    mslnpidfiqdqafqgiklheltlrgnfnssnimktclqnlaglhvhrlilgefkdernl
    eifepsimeglcdvtidefrltytndfsddivkfhclanvsamslagvsikyledvpkhf
    kwqslsiircqlkqfptldlpflksltltmnkgsisfkkvalpslsyldlsrnalsfsgc
    csysdlgtnslrhldlsfngaiimsanfmgleelqhldfqhstlkrvtefsaflslekll
    yldisytntkidfdgiflgltslntlkmagnsfkdntlsnvfanttnltfldlskcqleq
    iswgvfdtlhrlqllnmshnnllfldsshynqlyslkelaldtnqlksvpdgifdrltsl
    qkiwlhtnpwdcscpridylsrwlnknsqkeqgsakcsgsgkpvrsiicp
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >5ijdB (B:)
    npcievvpnityqcmdqklskvpddipsstknidlsfnplkilksysfsnfselqwldls
    rceietiedkawhglhhlsnliltgnpiqsfspgsfsgltslenlvavetklaslesfpi
    gqlitlkklnvahnfihscklpayfsnltnlvhvdlsynyiqtitvndlqflrenpqvnl
    sldmslnpidfiqdqafqgiklheltlrgnfnssnimktclqnlaglhvhrlilgefkde
    rnleifepsimeglcdvtidefrltytndfsddivkfhclanvsamslagvsikyledvp
    khfkwqslsiircqlkqfptldlpflksltltmnkgsisfkkvalpslsyldlsrnalsf
    sgccsysdlgtnslrhldlsfngaiimsanfmgleelqhldfqhstlkrvtefsaflsle
    kllyldisytntkidfdgiflgltslntlkmagnsfkdntlsnvfanttnltfldlskcq
    leqiswgvfdtlhrlqllnmshnnllfldsshynqlyslkelaldtnqlksvpdgifdrl
    tslqkiwlhtnpwdcscpridylsrwlnknsqkeqgsakcsgsgkpvrsiicpt
    

    Sequence, based on observed residues (ATOM records):
    >5ijdB (B:)
    pcievvpnityqcmdqklskvpddipsstknidlsfnplkilksysfsnfselqwldlsr
    ceietiedkawhglhhlsnliltgnpiqsfspgsfsgltslenlvavetklaslesfpig
    qlitlkklnvahnfihscklpayfsnltnlvhvdlsynyiqtitvndlqflrenpqvnls
    ldmslnpidfiqdqafqgiklheltlrgnfnssnimktclqnlaglhvhrlilgefkder
    nleifepsimeglcdvtidefrltytndfsddivkfhclanvsamslagvsikyledvpk
    hfkwqslsiircqlkqfptldlpflksltltmnkgsisfkkvalpslsyldlsrnalsfs
    gccsysdlgtnslrhldlsfngaiimsanfmgleelqhldfqhstlkrvtefsaflslek
    llyldisytntkidfdgiflgltslntlkmagnsfkdntlsnvfanttnltfldlskcql
    eqiswgvfdtlhrlqllnmshnnllfldsshynqlyslkelaldtnqlksvpdgifdrlt
    slqkiwlhtnpwdcscpridylsrwlnknsqkeqgsakcsgsgkpvrsiicp
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >5ijdC (C:)
    ekqqwfcnssdaiisysycdhlkfpisissepcirlrgtngfvhvefiprgnlkylyfnl
    fisvnsielpkrkevlchghdddysfcralkgetvntsipfsfegilfpkghyrcvaeai
    agdteeklfclnftiihrrdvnkgenlyfq
    

    Sequence, based on observed residues (ATOM records):
    >5ijdC (C:)
    kqqwfcnssdaiisysycdhlkfpisissepcirlrgtngfvhvefiprgnlkylyfnlf
    isvnsielpkrkevlchghdddysfcralkgetvntsipfsfegilfpkghyrcvaeaia
    gdteeklfclnftiihr
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >5ijdD (D:)
    ekqqwfcnssdaiisysycdhlkfpisissepcirlrgtngfvhvefiprgnlkylyfnl
    fisvnsielpkrkevlchghdddysfcralkgetvntsipfsfegilfpkghyrcvaeai
    agdteeklfclnftiihrrdvnkgenlyfq
    

    Sequence, based on observed residues (ATOM records):
    >5ijdD (D:)
    kqqwfcnssdaiisysycdhlkfpisissepcirlrgtngfvhvefiprgnlkylyfnlf
    isvnsielpkrkevlchghdddysfcralkgetvntsipfsfegilfpkghyrcvaeaia
    gdteeklfclnftiihr