PDB entry 4nqd

View 4nqd on RCSB PDB site
Description: Crystal structure of TCR-MR1 ternary complex and non-covalently bound 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil
Class: immune system
Keywords: immune complex, MR1, T-Cell receptor, Ig-domain, protein binding, Schiff base, membrane, IMMUNE SYSTEM
Deposited on 2013-11-25, released 2014-04-16
The last revision prior to the SCOPe 2.06 freeze date was dated 2014-11-19, with a file datestamp of 2014-11-14.
Experiment type: XRAY
Resolution: 2.2 Å
R-factor: 0.184
AEROSPACI score: 0.33 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Major histocompatibility complex class I-related gene protein
    Species: Homo sapiens [TaxId:9606]
    Gene: MR1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q95460 (1-End)
      • engineered mutation (261)
    Domains in SCOPe 2.06: d4nqda1, d4nqda2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, BETA-2 MICROGLOBULIN, CDABP0092, HDCMA22P
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d4nqdb_
  • Chain 'C':
    Compound: Major histocompatibility complex class I-related gene protein
    Species: Homo sapiens [TaxId:9606]
    Gene: MR1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q95460 (1-End)
      • expression tag (0)
      • engineered mutation (261)
    Domains in SCOPe 2.06: d4nqdc1, d4nqdc2
  • Chain 'D':
    Compound: TcR alpha chain
    Species: Homo sapiens [TaxId:9606]
    Gene: TCR-alpha
    Database cross-references and differences (RAF-indexed):
    • PDB 4NQD (0-End)
    Domains in SCOPe 2.06: d4nqdd1
  • Chain 'E':
    Compound: TCR beta chain
    Species: Homo sapiens [TaxId:9606]
    Gene: TCR-beta
    Database cross-references and differences (RAF-indexed):
    • PDB 4NQD
    Domains in SCOPe 2.06: d4nqde1, d4nqde2
  • Chain 'F':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, BETA-2 MICROGLOBULIN, CDABP0092, HDCMA22P
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d4nqdf_
  • Chain 'G':
    Compound: TcR alpha chain
    Species: Homo sapiens [TaxId:9606]
    Gene: TCR-alpha
    Database cross-references and differences (RAF-indexed):
    • PDB 4NQD (0-End)
    Domains in SCOPe 2.06: d4nqdg1, d4nqdg2
  • Chain 'H':
    Compound: TCR beta chain
    Species: Homo sapiens [TaxId:9606]
    Gene: TCR-beta
    Database cross-references and differences (RAF-indexed):
    • PDB 4NQD
    Domains in SCOPe 2.06: d4nqdh1, d4nqdh2
  • Heterogens: 2LJ, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4nqdA (A:)
    mrthslryfrlgvsdpihgvpefisvgyvdshpittydsvtrqkeprapwmaenlapdhw
    erytqllrgwqqmfkvelkrlqrhynhsgshtyqrmigcelledgsttgflqyaydgqdf
    lifnkdtlswlavdnvahtikqaweanqhellyqknwleeeciawlkrfleygkdtlqrt
    epplvrvnrketfpgvtalfckahgfyppeiymtwmkngeeivqeidygdilpsgdgtyq
    awasieldpqssnlyschvehsgvhmvlqvp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4nqdA (A:)
    rthslryfrlgvsdpihgvpefisvgyvdshpittydsvtrqkeprapwmaenlapdhwe
    rytqllrgwqqmfkvelkrlqrhynhsgshtyqrmigcelledgsttgflqyaydgqdfl
    ifnkdtlswlavdnvahtikqaweanqhellyqknwleeeciawlkrfleygkdtlqrte
    pplvrvnrketfpgvtalfckahgfyppeiymtwmkngeeieidygdilpsgdgtyqawa
    sielyschvehsgvhmvlqv
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4nqdB (B:)
    iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
    sfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >4nqdB (B:)
    iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
    sfyllyyteftptekdeyacrvnhvtlsqpkivkwd
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4nqdC (C:)
    mrthslryfrlgvsdpihgvpefisvgyvdshpittydsvtrqkeprapwmaenlapdhw
    erytqllrgwqqmfkvelkrlqrhynhsgshtyqrmigcelledgsttgflqyaydgqdf
    lifnkdtlswlavdnvahtikqaweanqhellyqknwleeeciawlkrfleygkdtlqrt
    epplvrvnrketfpgvtalfckahgfyppeiymtwmkngeeivqeidygdilpsgdgtyq
    awasieldpqssnlyschvehsgvhmvlqvp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4nqdC (C:)
    mrthslryfrlgvsdpivpefisvgyvdshpittydsvtrqkeprapwmaenlapdhwer
    ytqllrgwqqmfkvelkrlqrhynhsgshtyqrmigcelledgsttgflqyaydgqdfli
    fnkdtlswlavdnvahtikqaweanqhellyqknwleeeciawlkrfleygkdtlqrtep
    plvrvnralfckahgfyppeiymtwmknidygdilpsgdgtyqawasiesnlyschvehs
    gvhmvlqv
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4nqdD (D:)
    gqnidqptemtategaivqinctyqtsgfnglfwyqqhageaptflsynvldgleekgrf
    ssflsrskgysylllkelqmkdsasylcavkdsnyqliwgagtkliikpdiqnpdpavyq
    lrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsnksdf
    acanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >4nqdD (D:)
    gqnidqptemtategaivqinctyqtsgfnglfwyqqhageaptflsynvldgleekgrf
    ssflsrskgysylllkelqmkdsasylcavkdsnyqliwgagtkliikpdiqnpdpavyq
    lrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsnksdf
    acanafnnsiipedtffpsp
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >4nqdE (E:)
    nagvtqtpkfqvlktgqsmtlqcaqdmnhnsmywyrqdpgmglrliyysasegttdkgev
    pngynvsrlnkrefslrlesaapsqtsvyfcassvwtgegsgelffgegsrltvledlkn
    vfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplke
    qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
    wgrad
    

    Sequence, based on observed residues (ATOM records): (download)
    >4nqdE (E:)
    agvtqtpkfqvlktgqsmtlqcaqdmnhnsmywyrqdpgmglrliyysasegttdkgevp
    ngynvsrlnkrefslrlesaapsqtsvyfcassvwtgegsgelffgegsrltvledlknv
    fppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeq
    palndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeaw
    gra
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >4nqdF (F:)
    iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
    sfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >4nqdF (F:)
    iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
    sfyllyyteftptekdeyacrvnhvtlsqpkivkwdr
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >4nqdG (G:)
    gqnidqptemtategaivqinctyqtsgfnglfwyqqhageaptflsynvldgleekgrf
    ssflsrskgysylllkelqmkdsasylcavkdsnyqliwgagtkliikpdiqnpdpavyq
    lrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsnksdf
    acanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >4nqdG (G:)
    gqnidqptemtategaivqinctyqtsgfnglfwyqqhageaptflsynvldgleekgrf
    ssflsrskgysylllkelqmkdsasylcavkdsnyqliwgagtkliikpdiqnpdpavyq
    lrdsvclftdfdsqtnvsqsdvyitdkcvldmrsmdfksnsavawsnksdfacanafnns
    iipedtffps
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >4nqdH (H:)
    nagvtqtpkfqvlktgqsmtlqcaqdmnhnsmywyrqdpgmglrliyysasegttdkgev
    pngynvsrlnkrefslrlesaapsqtsvyfcassvwtgegsgelffgegsrltvledlkn
    vfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplke
    qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
    wgrad
    

    Sequence, based on observed residues (ATOM records): (download)
    >4nqdH (H:)
    gvtqtpkfqvlktgqsmtlqcaqdmnhnsmywyrqdpgmglrliyysasegttdkgevpn
    gynvsrlnkrefslrlesaapsqtsvyfcassvwtgegsgelffgegsrltvledlknvf
    ppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqp
    alndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawg
    ra