PDB entry 5wlg

View 5wlg on RCSB PDB site
Description: Crystal Structure of H-2Db with the GAP501 peptide (SQL)
Class: immune system
Keywords: H-2Db, malaria, GAP50, Immune response gene, TCR, T cell, Vb8.1, IMMUNE SYSTEM
Deposited on 2017-07-26, released 2017-11-15
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-05-29, with a file datestamp of 2019-05-24.
Experiment type: XRAY
Resolution: 2.1 Å
R-factor: N/A
AEROSPACI score: 0.28 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: H-2 class I histocompatibility antigen, D-B alpha chain
    Species: Mus musculus [TaxId:10090]
    Gene: H2-D1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5wlga1, d5wlga2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5wlgb_
  • Chain 'C':
    Compound: GAP50 peptide
    Species: Plasmodium berghei [TaxId:5821]
    Gene: GAP50, PBK173_000161900, PBNK65E_000154900, PBNK65NY_000154100, PBSP11A_000154100, PBSP11RLL_000154100
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: T cell receptor alpha variable 8D-2,Human nkt tcr alpha chain
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • Uniprot A0A075B616 (0-86)
      • linker (86-104)
      • linker (87-105)
    • Uniprot K7N5M3 (106-End)
    Domains in SCOPe 2.08: d5wlgd1, d5wlgd2
  • Chain 'E':
    Compound: T-cell receptor beta chain V region C5,Human nkt tcr beta chain
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • Uniprot P04213 (0-112)
      • conflict (94-95)
      • insertion (99)
      • insertion (101)
      • conflict (105)
      • conflict (107-108)
      • conflict (110)
    • Uniprot K7N5M4 (113-242)
    Domains in SCOPe 2.08: d5wlge1, d5wlge2
  • Chain 'F':
    Compound: H-2 class I histocompatibility antigen, D-B alpha chain
    Species: Mus musculus [TaxId:10090]
    Gene: H2-D1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5wlgf1, d5wlgf2
  • Chain 'G':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5wlgg_
  • Chain 'H':
    Compound: GAP50 peptide
    Species: Plasmodium berghei [TaxId:5821]
    Gene: GAP50, PBK173_000161900, PBNK65E_000154900, PBNK65NY_000154100, PBSP11A_000154100, PBSP11RLL_000154100
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: T cell receptor alpha variable 8D-2,Human nkt tcr alpha chain
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • Uniprot A0A075B616 (Start-85)
      • linker (85-103)
      • linker (86-104)
    • Uniprot K7N5M3 (105-End)
    Domains in SCOPe 2.08: d5wlgi1, d5wlgi2
  • Chain 'J':
    Compound: T-cell receptor beta chain V region C5,Human nkt tcr beta chain
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • Uniprot P04213 (Start-112)
      • conflict (94-95)
      • insertion (99)
      • insertion (101)
      • conflict (105)
      • conflict (107-108)
      • conflict (110)
    • Uniprot K7N5M4 (113-242)
    Domains in SCOPe 2.08: d5wlgj1, d5wlgj2
  • Heterogens: NA, CL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5wlgA (A:)
gphsmryfetavsrpgleepryisvgyvdnkefvrfdsdaenpryeprapwmeqegpeyw
eretqkakgqeqwfrvslrnllgyynqsaggshtlqqmsgcdlgsdwrllrgylqfayeg
rdyialnedlktwtaadmaaqitrrkweqsgaaehykaylegecvewlhrylkngnatll
rtdspkahvthhprskgevtlrcwalgfypaditltwqlngeeltqdmelvetrpagdgt
fqkwasvvvplgkeqnytcrvyheglpepltlrweppp

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >5wlgB (B:)
iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
sfyilahteftptetdtyacrvkhasmaepktvywdrdm

    Sequence, based on observed residues (ATOM records): (download) 
    >5wlgB (B:)
qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
fyilahteftptetdtyacrvkhasmaepktvywdrdm

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5wlgD (D:)
enlqalsiqegedvtmncsyktyttvvhwyrqdsgrgpaliilirsnerekrsgrlratl
dtssqssslsitaaqcedtavyfcatvyaqgltfglgtrvsvfpniqnpdpavyqlrdsk
ssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsnksdfacana
fn

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5wlgE (E:)
eaavtqsprskvavtggkvtlschqtnnhdymywyrqdtghglrlihysyvadstekgdi
pdgykasrpsqenfslilelaslsqtavyfcassdwgdtgqlyfgegskltvledlknvf
ppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqp
alndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawg
rad

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >5wlgF (F:)
gphsmryfetavsrpgleepryisvgyvdnkefvrfdsdaenpryeprapwmeqegpeyw
eretqkakgqeqwfrvslrnllgyynqsaggshtlqqmsgcdlgsdwrllrgylqfayeg
rdyialnedlktwtaadmaaqitrrkweqsgaaehykaylegecvewlhrylkngnatll
rtdspkahvthhprskgevtlrcwalgfypaditltwqlngeeltqdmelvetrpagdgt
fqkwasvvvplgkeqnytcrvyheglpepltlrweppp

    Sequence, based on observed residues (ATOM records): (download) 
    >5wlgF (F:)
gphsmryfetavsrpgleepryisvgyvdnkefvrfdsdaenpryeprapwmeqegpeyw
eretqkakgqeqwfrvslrnllgyynqsaggshtlqqmsgcdlgsdwrllrgylqfayeg
rdyialnedlktwtaadmaaqitrrkweqsgaaehykaylegecvewlhrylkngnatll
rtdspkahvthhprskgevtlrcwalgfypaditltwqlngeeltqdmelvetrpagdgt
fqkwasvvvplgkeqnytcrvyheglpepltlrwepp

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >5wlgG (G:)
iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
sfyilahteftptetdtyacrvkhasmaepktvywdrdm

    Sequence, based on observed residues (ATOM records): (download) 
    >5wlgG (G:)
qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
fyilahteftptetdtyacrvkhasmaepktvywdrdm

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >5wlgI (I:)
enlqalsiqegedvtmncsyktyttvvhwyrqdsgrgpaliilirsnerekrsgrlratl
dtssqssslsitaaqcedtavyfcatvyaqgltfglgtrvsvfpniqnpdpavyqlrdsk
ssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsnksdfacana
fn

    Sequence, based on observed residues (ATOM records): (download) 
    >5wlgI (I:)
qalsiqegedvtmncsyktyttvvhwyrqdsgrgpaliilirsnerekrsgrlratldts
sqssslsitaaqcedtavyfcatvyaqgltfglgtrvsvfpniqnpdpavyqlrdskssd
ksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsnksdfacana

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >5wlgJ (J:)
eaavtqsprskvavtggkvtlschqtnnhdymywyrqdtghglrlihysyvadstekgdi
pdgykasrpsqenfslilelaslsqtavyfcassdwgdtgqlyfgegskltvledlknvf
ppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqp
alndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawg
rad

    Sequence, based on observed residues (ATOM records): (download) 
    >5wlgJ (J:)
avtqsprskvavtggkvtlschqtnnhdymywyrqdtghglrlihysyvadstekgdipd
gykasrpsqenfslilelaslsqtavyfcassdwgdtgqlyfgegskltvledlknvfpp
evavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpal
ndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra
d