PDB entry 4mng

View 4mng on RCSB PDB site
Description: Structure of the DP10.7 TCR with CD1d-sulfatide
Class: immune system
Keywords: Immunglobulin, Histocompatibility Antigens, CD1, Immunological, lymphocytes, gamma delta T cell, T cell recognition, self-recognition, myelin, intestinal epithelial lymphocytes, Human, Lipid binding, self-ligand,, Glycoproteins, Cell-surface receptors, IMMUNE SYSTEM
Deposited on 2013-09-10, released 2013-12-18
The last revision prior to the SCOPe 2.04 freeze date was dated 2014-01-01, with a file datestamp of 2013-12-27.
Experiment type: XRAY
Resolution: 3.01 Å
R-factor: 0.179
AEROSPACI score: 0.22 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Antigen-presenting glycoprotein CD1d, Cd1d1 protein
    Species: HOMO SAPIENS, MUS MUSCULUS [TaxId:9606, 10090]
    Gene: CD1D, Cd1d1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P15813 (Start-183)
    • Uniprot Q7TMK5 (184-277)
      • expression tag (278)
    Domains in SCOPe 2.04: d4mnga1, d4mnga2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d4mngb_
  • Chain 'C':
    Compound: Antigen-presenting glycoprotein CD1d, Cd1d1 protein
    Species: HOMO SAPIENS, MUS MUSCULUS [TaxId:9606, 10090]
    Gene: CD1D, Cd1d1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P15813 (Start-183)
    • Uniprot Q7TMK5 (184-277)
      • expression tag (278)
    Domains in SCOPe 2.04: d4mngc1, d4mngc2
  • Chain 'D':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d4mngd_
  • Chain 'E':
    Compound: TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region
    Species: Homo sapiens [TaxId:9606]
    Gene: TRA@
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q6PJ56 (Start-118)
      • conflict (96-99)
      • conflict (101-102)
      • conflict (104-106)
    • PDB 4MNG (Start-255)
      • engineered mutation (250)
      • engineered mutation (252-253)
    Domains in SCOPe 2.04: d4mnge1, d4mnge2
  • Chain 'F':
    Compound: TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region
    Species: Homo sapiens [TaxId:9606]
    Gene: TRA@
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q6PJ56 (Start-118)
      • conflict (96-99)
      • conflict (101-102)
      • conflict (104-106)
    • PDB 4MNG (Start-255)
      • engineered mutation (250)
      • engineered mutation (252-253)
    Domains in SCOPe 2.04: d4mngf1, d4mngf2
  • Heterogens: NAG, CIS, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4mngA (A:)
    adpvpqrlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfs
    dqqwetlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafq
    gkdilsfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgks
    elkkqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpna
    detwylqatldveageeaglacrvkhsslggqdiilywsgr
    

    Sequence, based on observed residues (ATOM records): (download)
    >4mngA (A:)
    rlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqwet
    lqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafqgkdils
    fqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkkqe
    kpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwyl
    qatldveageeaglacrvkhsslggqdiilyws
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >4mngB (B:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4mngC (C:)
    adpvpqrlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfs
    dqqwetlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafq
    gkdilsfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgks
    elkkqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpna
    detwylqatldveageeaglacrvkhsslggqdiilywsgr
    

    Sequence, based on observed residues (ATOM records): (download)
    >4mngC (C:)
    rlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqwet
    lqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafqgkdils
    fqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkkqe
    kpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwyl
    qatldveageeaglacrvkhsslggqdiilyws
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download)
    >4mngD (D:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >4mngE (E:)
    aqkvtqaqssvsmpvrkavtlnclyetswwsyyifwykqlpskemiflirqgsdeqnaks
    grysvnfkkaaksvaltisalqledsakyfcalgepsywgfprttrvifgkgtrvtvepg
    gggsggggsggggsggggsssnlegrtksvirqtgssaeitcdlaegstgyihwylhqeg
    kapqrllyydsytssvvlesgispgkydtygstrknlrmilrnliendsgvyycatwdek
    yykklfgsgtkliitdaasgad
    

    Sequence, based on observed residues (ATOM records): (download)
    >4mngE (E:)
    qkvtqaqssvsmpvrkavtlnclyetswwsyyifwykqlpskemiflirqgsdeqnaksg
    rysvnfkkaaksvaltisalqledsakyfcalgepsywgfprttrvifgkgtrvtveptk
    svirqtgssaeitcdlaegstgyihwylhqegkapqrllyydsytssvvlesgispgkyd
    tygstrknlrmilrnliendsgvyycatwdekyykklfgsgtkliitd
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >4mngF (F:)
    aqkvtqaqssvsmpvrkavtlnclyetswwsyyifwykqlpskemiflirqgsdeqnaks
    grysvnfkkaaksvaltisalqledsakyfcalgepsywgfprttrvifgkgtrvtvepg
    gggsggggsggggsggggsssnlegrtksvirqtgssaeitcdlaegstgyihwylhqeg
    kapqrllyydsytssvvlesgispgkydtygstrknlrmilrnliendsgvyycatwdek
    yykklfgsgtkliitdaasgad
    

    Sequence, based on observed residues (ATOM records): (download)
    >4mngF (F:)
    qkvtqaqssvsmpvrkavtlnclyetswwsyyifwykqlpskemiflirqgsdeqnaksg
    rysvnfkkaaksvaltisalqledsakyfcalgepsywgfprttrvifgkgtrvtveptk
    svirqtgssaeitcdlaegstgyihwylhqegkapqrllyydsytssvvlesgispgkyd
    tygstrknlrmilrnliendsgvyycatwdekyykklfgsgtkliitd