SMTL ID : 9qg8.1

Crystal structure of the great reed warbler MHC class I in complex with an 8-mer peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

1 x LYS- THR- MET- MET- ALA- HIS- ASP- LEU: LYS-THR-MET-MET-ALA-HIS-ASP-LEU(Non-covalent)

LYS-THR-MET-MET-ALA-HIS-ASP-LEU.1: 26 residues within 4Å: Chain A: Y.8, M.44, S.62, Q.63, I.66, G.69, S.70, V.73, Y.74, R.76, S.77, L.81, R.84, R.96, Y.98, E.112, F.121, T.141, R.144, W.145, V.151, R.154, Q.155, Y.158, W.166, Y.170 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.8, A:Q.63, A:I.66, A:L.81, A:F.121, A:Y.158, A:W.166, A:W.166 Hydrogen bonds: A:Y.8, A:S.62, A:S.62, A:Q.63, A:S.70, A:V.73, A:S.77, A:R.96, A:R.96, A:Y.98, A:Y.98, A:Q.155, A:Y.170, A:Y.170 Water bridges: A:T.80 Salt bridges: A:R.76, A:R.84, A:R.144

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: L.6, H.7, G.99, C.100, E.101, R.109, G.110, S.111 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.101, A:R.109 Water bridges: A:V.97, A:S.111 GOL.3: 4 residues within 4Å: Chain A: P.183, Y.204, G.205 Chain B: R.35 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.35, B:R.35, A:G.205 GOL.4: 5 residues within 4Å: Chain A: I.211, A.212, V.213, N.214, W.228 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.211, A:V.213, A:N.214, A:W.228 GOL.5: 2 residues within 4Å: Chain A: L.102, Q.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.168 GOL.6: 5 residues within 4Å: Chain A: W.242, R.244 Chain B: V.32, Y.33 Ligands: GOL.7 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:V.32, A:R.244, A:R.244 GOL.7: 8 residues within 4Å: Chain A: H.202, Y.204 Chain B: Y.33, A.34, W.118, E.119, D.121 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.34, B:A.34, B:W.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Venskutonyte, R. et al., MHC I of the Great Reed Warbler Promotes a Flat Peptide Binding Mode. Immunology (2025)

Release Date

2025-07-23

Peptides

MHC class I antigen: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MHC class I antigen

Beta-2-microglobulin

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