SMTL ID : 5wli.3 (3 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-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: 31 residues within 4Å: Chain A: M.5, Y.7, E.9, Y.22, S.24, Y.45, E.63, K.66, A.67, Q.70, W.73, V.76, S.77, N.80, Y.84, L.95, Q.97, S.99, F.116, Y.123, I.124, T.143, K.146, W.147, S.150, H.155, Y.156, Y.159, E.163, W.167, Y.171 39 PLIP interactions: 39 interactions with chain A Hydrophobic interactions: A:Y.7, A:K.66, A:W.73, A:W.73, A:V.76, A:V.76, A:L.95, A:Y.123, A:I.124, A:T.143, A:K.146, A:W.147, A:Y.159, A:Y.159 Hydrogen bonds: A:E.9, A:Y.22, A:S.24, A:E.63, A:K.66, A:Q.70, A:Q.70, A:S.77, A:N.80, A:Y.84, A:Q.97, A:Q.97, A:T.143, A:K.146, A:Y.156, A:Y.156, A:Y.159, A:Y.171 Water bridges: A:E.63, A:K.66, A:S.99, A:S.99, A:H.155, A:Y.159 Salt bridges: A:K.146

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 3 residues within 4Å: Chain A: D.238 Chain B: R.12, H.13 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.13 Salt bridges: B:R.12, B:H.13

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

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

Beta-2-microglobulin

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