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):
- 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):
- 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):
- 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):
- 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.