SMTL ID : 7zqj.1

MHC class I from a wild bird in complex with a nonameric peptide P3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MET- THR- MET- ILE- THR- PRO- PRO- THR- PHE: Uncharacterized protein Rv3403c(Non-covalent)

MET-THR-MET-ILE-THR-PRO-PRO-THR-PHE.1: 30 residues within 4Å: Chain A: L.6, Y.8, A.25, M.44, Y.59, S.62, Q.63, I.66, G.67, S.70, V.73, Y.74, S.77, T.80, L.81, R.84, R.96, Y.98, F.114, F.121, T.141, R.144, W.145, V.151, R.154, Q.155, Y.158, E.162, W.166, Y.170 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:Y.59, A:I.66, A:V.73, A:Y.74, A:L.81, A:Y.98, A:F.114, A:F.114, A:F.121, A:F.121, A:T.141, A:W.145, A:V.151, A:Y.158, A:Y.158, A:Y.158 Hydrogen bonds: A:Y.8, A:Q.63, A:S.77, A:T.80, A:T.80, A:R.96, A:R.96, A:Y.98, A:Y.98, A:R.144, A:R.154, A:R.154, A:Y.158, A:W.166, A:Y.170 Water bridges: A:S.77, A:W.166 Salt bridges: A:R.84, A:R.144

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: V.97, R.113 Chain B: F.79, N.80, D.81 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.113 Salt bridges: A:R.113

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 6 residues within 4Å: Chain A: E.182, P.183, D.185, Y.204, G.205 Chain B: R.35 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.182, A:P.183, A:D.185 Water bridges: B:R.35, B:R.35 Salt bridges: B:R.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eltschkner, S. et al., The structure of songbird MHC class I reveals antigen binding that is flexible at the N-terminus and static at the C-terminus. Front Immunol (2023)

Release Date

2023-05-10

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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