SMTL ID : 5wlg.2 (1 other biounit)

Crystal Structure of H-2Db with the GAP501 peptide (SQL)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x SER- GLN- LEU- LEU- ASN- ALA- LYS- TYR- LEU: GAP50 peptide(Non-covalent)

SER-GLN-LEU-LEU-ASN-ALA-LYS-TYR-LEU.1: 41 residues within 4Å: Chain A: M.5, Y.7, E.9, Y.22, S.24, Y.45, R.62, E.63, K.66, Q.70, Q.72, W.73, V.76, S.77, N.80, L.81, Y.84, L.95, Q.97, S.99, L.114, F.116, Y.123, T.143, K.146, W.147, S.150, H.155, Y.156, Y.159, E.163, W.167, Y.171 Chain C: A.89, Q.90 Chain D: N.28, D.30, Y.31, Y.50, D.95, W.96 44 PLIP interactions: 36 interactions with chain A, 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: A:Y.7, A:W.73, A:W.73, A:V.76, A:V.76, A:L.81, A:L.95, A:L.114, A:Y.123, A:T.143, A:W.147, A:Y.159, A:Y.159, D:D.30, D:W.96, C:Q.90 Hydrogen bonds: A:E.9, A:Y.22, A:S.24, A:Y.45, A:R.62, A:E.63, A:K.66, A:Q.70, A:Q.70, A:S.77, A:N.80, A:Q.97, A:Q.97, A:T.143, A:K.146, A:Y.156, A:Y.159, A:E.163, A:Y.171, D:D.30, D:Y.50, D:D.95 Water bridges: A:K.66, A:H.155, A:Y.159, D:D.30, D:Q.71 Salt bridges: A:K.146

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 2 residues within 4Å: Chain B: S.52, D.53 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.52, B:S.52 Water bridges: A:R.35 NA.3: 3 residues within 4Å: Chain C: C.127, F.129, A.168 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:C.127, C:F.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Braeckel-Budimir, N. et al., A T Cell Receptor Locus Harbors a Malaria-Specific Immune Response Gene. Immunity (2017)

Release Date

2017-11-15

Peptides

H-2 class I histocompatibility antigen, D-B alpha chain: A
Beta-2-microglobulin: B
T cell receptor alpha variable 8D-2,Human nkt tcr alpha chain: C
T-cell receptor beta chain V region C5,Human nkt tcr beta chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
I

D
J

H-2 class I histocompatibility antigen, D-B alpha chain

Beta-2-microglobulin

T cell receptor alpha variable 8D-2,Human nkt tcr alpha chain

T-cell receptor beta chain V region C5,Human nkt tcr beta chain

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