SMTL ID : 5npz.1

Porcine (Sus scrofa) Major Histocompatibility Complex, class I, presenting EFEDLTFLA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLU- PHE- GLU- ASP- LEU- THR- PHE- LEU- ALA: GLU-PHE-GLU-ASP-LEU-THR-PHE-LEU-ALA(Non-covalent)

GLU-PHE-GLU-ASP-LEU-THR-PHE-LEU-ALA.1: 28 residues within 4Å: Chain A: L.6, Y.8, M.46, Y.60, R.63, N.64, N.67, V.68, S.71, I.74, V.77, N.78, T.81, L.82, Y.85, W.98, Y.100, S.144, K.147, W.148, A.153, H.156, W.157, Y.160, T.164, S.168, Y.172 Ligands: EDO.9 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:V.68, A:I.74, A:V.77, A:L.82, A:W.98, A:W.98, A:A.153, A:T.164 Hydrogen bonds: A:Y.8, A:N.64, A:N.64, A:N.78, A:N.78, A:Y.85, A:Y.100, A:Y.100, A:S.144, A:Y.160, A:S.168, A:Y.172 Water bridges: A:R.63, A:R.63, A:N.64, A:N.67, A:N.67, A:T.81, A:H.156 Salt bridges: A:R.63, A:K.147, A:H.156 pi-Stacking: A:Y.8

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: R.36, E.47, P.48, R.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.49 EDO.5: 7 residues within 4Å: Chain A: R.22, I.24 Chain B: Q.51, S.52, D.53, L.54, L.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.51, B:L.54 Water bridges: B:D.53 EDO.6: 8 residues within 4Å: Chain A: W.205, L.207, R.235, Q.243 Chain B: Y.11, S.12, H.14, P.15 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.12, B:H.14, A:R.235, A:Q.243 EDO.7: 5 residues within 4Å: Chain B: K.42, M.47, F.70, T.71, Y.78 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.42, B:T.71, B:T.71, B:Y.78 EDO.9: 4 residues within 4Å: Chain A: K.147, W.148 Ligands: GLU-PHE-GLU-ASP-LEU-THR-PHE-LEU-ALA.1, GLU-PHE-GLU-ASP-LEU-THR-PHE-LEU-ALA.1 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: A.126, L.127, N.128, T.135 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.127, A:T.135 Water bridges: A:Q.116 GOL.8: 4 residues within 4Å: Chain B: V.85, T.86, L.87, D.88 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.86

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: R.36, F.37, D.38, A.41, E.47 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.36, A:E.47 Water bridges: A:R.36, A:D.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tungatt, K. et al., Induction of influenza-specific local CD8 T-cells in the respiratory tract after aerosol delivery of vaccine antigen or virus in the Babraham inbred pig. Plos Pathog. (2018)

Release Date

2018-05-02

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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