PDB entry 5kd7

View 5kd7 on RCSB PDB site
Description: Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PV9) of HIV gp120 MN Isolate (IGPGRAFYV)
Class: immune system
Keywords: MAJOR HISTOMPATIBILITY COMPLEX CLASS I, MHC-I, H2-Dd, H-2Dd, HIV peptide, PVI10, PV9, GLYCOPROTEIN, IMMUNE RESPONSE, IMMUNE SYSTEM
Deposited on 2016-06-07, released 2017-10-11
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-02-19, with a file datestamp of 2020-02-14.
Experiment type: XRAY
Resolution: 2.35 Å
R-factor: N/A
AEROSPACI score: 0.24 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: H-2 class I histocompatibility antigen, D-D alpha chain
    Species: Mus musculus [TaxId:10090]
    Gene: H2-D1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kd7a1, d5kd7a2
  • 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: d5kd7b_
  • Chain 'C':
    Compound: H-2 class I histocompatibility antigen, D-D alpha chain
    Species: Mus musculus [TaxId:10090]
    Gene: H2-D1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kd7c1, d5kd7c2
  • Chain 'D':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (1-99)
      • initiating methionine (0)
    Domains in SCOPe 2.08: d5kd7d1, d5kd7d2
  • Chain 'E':
    Compound: Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)
    Species: Human immunodeficiency virus type 1 group M subtype B (isolate MN) [TaxId:11696]
    Database cross-references and differences (RAF-indexed):
    • PDB 5KD7 (0-8)
  • Chain 'F':
    Compound: H-2 class I histocompatibility antigen, D-D alpha chain
    Species: Mus musculus [TaxId:10090]
    Gene: H2-D1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kd7f1, d5kd7f2
  • Chain 'G':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (1-99)
      • initiating methionine (0)
    Domains in SCOPe 2.08: d5kd7g1, d5kd7g2
  • Chain 'H':
    Compound: Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)
    Species: Human immunodeficiency virus type 1 group M subtype B (isolate MN) [TaxId:11696]
    Database cross-references and differences (RAF-indexed):
    • PDB 5KD7 (0-8)
  • Chain 'I':
    Compound: H-2 class I histocompatibility antigen, D-D alpha chain
    Species: Mus musculus [TaxId:10090]
    Gene: H2-D1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kd7i1, d5kd7i2
  • Chain 'J':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (1-99)
      • initiating methionine (0)
    Domains in SCOPe 2.08: d5kd7j1, d5kd7j2
  • Chain 'K':
    Compound: Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)
    Species: Human immunodeficiency virus type 1 group M subtype B (isolate MN) [TaxId:11696]
    Database cross-references and differences (RAF-indexed):
    • PDB 5KD7 (0-8)
  • Chain 'P':
    Compound: Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)
    Species: Human immunodeficiency virus type 1 group M subtype B (isolate MN) [TaxId:11696]
    Database cross-references and differences (RAF-indexed):
    • PDB 5KD7 (0-8)
  • Heterogens: EDO, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >5kd7A (A:)
shslryfvtavsrpgfgeprymevgyvdntefvrfdsdaenpryeprarwieqegpeywe
retrrakgneqsfrvdlrtalryynqsaggshtlqwmagcdvesdgrllrgywqfaydgc
dyialnedlktwtaadmaaqitrrkweqagaaerdraylegecvewlrrylkngnatllr
tdppkahvthhrrpegdvtlrcwalgfypaditltwqlngeeltqemelvetrpagdgtf
qkwasvvvplgkeqkytchveheglpepltlrwgk

    Sequence, based on observed residues (ATOM records): (download) 
    >5kd7A (A:)
shslryfvtavsrpgfgeprymevgyvdntefvrfdsdaenpryeprarwieqegpeywe
retrrakgneqsfrvdlrtalryynqsaggshtlqwmagcdvesdgrllrgywqfaydgc
dyialnedlktwtaadmaaqitrrkweqagaaerdraylegecvewlrrylkngnatllr
tdppkahvthhrrpegdvtlrcwalgfypaditltwqlngeeltqemelvetrpagdgtf
qkwasvvvplgkeqkytchveheglpepltlrw

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >5kd7B (B:)
miqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskd
wsfyilahteftptetdtyacrvkhasmaepktvywdrdm

    Sequence, based on observed residues (ATOM records): (download) 
    >5kd7B (B:)
iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
sfyilahteftptetdtyacrvkhasmaepktvywdrdm

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >5kd7C (C:)
shslryfvtavsrpgfgeprymevgyvdntefvrfdsdaenpryeprarwieqegpeywe
retrrakgneqsfrvdlrtalryynqsaggshtlqwmagcdvesdgrllrgywqfaydgc
dyialnedlktwtaadmaaqitrrkweqagaaerdraylegecvewlrrylkngnatllr
tdppkahvthhrrpegdvtlrcwalgfypaditltwqlngeeltqemelvetrpagdgtf
qkwasvvvplgkeqkytchveheglpepltlrwgk

    Sequence, based on observed residues (ATOM records): (download) 
    >5kd7C (C:)
shslryfvtavsrpgfgeprymevgyvdntefvrfdsdaenpryeprarwieqegpeywe
retrrakgneqsfrvdlrtalryynqsaggshtlqwmagcdvesdgrllrgywqfaydgc
dyialnedlktwtaadmaaqitrrkweqagaaerdraylegecvewlrrylkngnatllr
tdppkahvthhrrpegdvtlrcwalgfypaditltwqlngeeltqemelvetrpagdgtf
qkwasvvvplgkeqkytchveheglpepltlrw

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5kd7D (D:)
miqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskd
wsfyilahteftptetdtyacrvkhasmaepktvywdrdm

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5kd7F (F:)
shslryfvtavsrpgfgeprymevgyvdntefvrfdsdaenpryeprarwieqegpeywe
retrrakgneqsfrvdlrtalryynqsaggshtlqwmagcdvesdgrllrgywqfaydgc
dyialnedlktwtaadmaaqitrrkweqagaaerdraylegecvewlrrylkngnatllr
tdppkahvthhrrpegdvtlrcwalgfypaditltwqlngeeltqemelvetrpagdgtf
qkwasvvvplgkeqkytchveheglpepltlrwgk

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5kd7G (G:)
miqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskd
wsfyilahteftptetdtyacrvkhasmaepktvywdrdm

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >5kd7I (I:)
shslryfvtavsrpgfgeprymevgyvdntefvrfdsdaenpryeprarwieqegpeywe
retrrakgneqsfrvdlrtalryynqsaggshtlqwmagcdvesdgrllrgywqfaydgc
dyialnedlktwtaadmaaqitrrkweqagaaerdraylegecvewlrrylkngnatllr
tdppkahvthhrrpegdvtlrcwalgfypaditltwqlngeeltqemelvetrpagdgtf
qkwasvvvplgkeqkytchveheglpepltlrwgk

    Sequence, based on observed residues (ATOM records): (download) 
    >5kd7I (I:)
shslryfvtavsrpgfgeprymevgyvdntefvrfdsdaenpryeprarwieqegpeywe
retrrakgneqsfrvdlrtalryynqsaggshtlqwmagcdvesdrllrgywqfaydgcd
yialnedlktwtaadmaaqitrrkweqagaaerdraylegecvewlrrylkngnatllrt
dppkahvthhrrgdvtlrcwalgfypaditltwqlngeeltqemelvetrpagdgtfqkw
asvvvplgkeqkytchveheltlrwg

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5kd7J (J:)
miqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskd
wsfyilahteftptetdtyacrvkhasmaepktvywdrdm

  • Chain 'K':
    No sequence available.

  • Chain 'P':
    No sequence available.