SMTL ID : 5nq0.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ASP- PHE- GLU- ARG- GLU- GLY- TYR- SER- LEU: ASP-PHE-GLU-ARG-GLU-GLY-TYR-SER-LEU(Non-covalent)

ASP-PHE-GLU-ARG-GLU-GLY-TYR-SER-LEU.1: 28 residues within 4Å: Chain A: L.5, Y.7, M.45, Y.59, R.62, N.63, N.66, V.67, S.70, I.73, N.77, T.80, L.81, Y.84, W.97, Y.99, F.116, L.124, S.143, K.146, W.147, A.150, A.152, H.155, W.156, Y.159, S.167, Y.171 40 PLIP interactions: 40 interactions with chain A Hydrophobic interactions: A:Y.7, A:N.66, A:V.67, A:I.73, A:L.81, A:W.97, A:W.97, A:L.124, A:W.147, A:A.150, A:A.152, A:W.156, A:Y.159, A:Y.159 Hydrogen bonds: A:Y.7, A:N.63, A:N.63, A:N.66, A:S.70, A:N.77, A:Y.99, A:Y.99, A:S.143, A:K.146, A:A.150, A:Y.159, A:S.167 Water bridges: A:Y.7, A:Y.7, A:N.77, A:W.97, A:H.155, A:Y.159, A:S.167, A:Y.171 Salt bridges: A:R.62, A:K.146, A:H.155 pi-Stacking: A:Y.7, A:Y.99

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: L.206, G.207, S.236, D.238, T.240, F.241, Q.242 Chain B: R.13, H.14 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.207, A:S.236, A:F.241, A:Q.242, B:R.13, B:H.14 Water bridges: A:D.238 GOL.3: 4 residues within 4Å: Chain A: P.47, Q.53, E.55, W.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.53, A:E.55 GOL.4: 8 residues within 4Å: Chain A: Y.85, Y.118, D.119, A.121, D.122, Y.123, A.136, D.137 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.118, A:D.122, A:A.136 GOL.10: 6 residues within 4Å: Chain B: I.38, D.39, K.46, A.49, Q.51, V.66 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.46, B:K.46 Water bridges: B:I.38, B:I.38, B:A.49, B:A.49, B:Q.51 GOL.11: 4 residues within 4Å: Chain B: V.85, T.86, L.87, D.88 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.88

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

EDO.5: 6 residues within 4Å: Chain A: P.47, R.48, A.49, P.50, Q.53 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.49 EDO.6: 5 residues within 4Å: Chain A: R.35, E.46, P.47, R.48 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.48 EDO.7: 5 residues within 4Å: Chain A: N.127, S.132, W.133, T.134, K.144 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.127, A:W.133, A:K.144 Water bridges: A:S.132, A:K.144, A:K.144, A:K.144, A:K.144 EDO.12: 8 residues within 4Å: Chain A: R.21, I.23 Chain B: Q.51, S.52, D.53, L.54, L.64 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.51, B:L.54 EDO.13: 7 residues within 4Å: Chain A: L.206, R.234, Q.242 Chain B: Y.11, S.12, H.14, P.15 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.12, A:R.234, A:Q.242, A:Q.242 Water bridges: B:H.99 EDO.14: 5 residues within 4Å: Chain B: K.83, H.84, L.87, K.89, P.90 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.84, B:H.84 EDO.15: 5 residues within 4Å: Chain B: N.48, A.49, E.50, H.67, T.68 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.50, B:H.67, B:T.68 Water bridges: B:E.50, B:E.69 EDO.16: 7 residues within 4Å: Chain B: P.34, Q.35, I.36, Q.51, L.54 Ligands: SO4.9, EDO.12 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:R.21 Hydrogen bonds: B:P.34, B:I.36, B:Q.51

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

SO4.8: 3 residues within 4Å: Chain A: R.35, A.40, E.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.46 Salt bridges: A:R.35 SO4.9: 6 residues within 4Å: Chain A: V.12, R.21, I.23 Chain B: P.34, Q.35 Ligands: EDO.16 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Water bridges: A:R.14, A:R.21, A:R.21, A:R.21 Salt bridges: A:R.21 Hydrogen bonds: B:P.34, B:Q.35 SO4.17: 7 residues within 4Å: Chain A: D.119, G.120, A.121 Chain B: M.1, V.2, R.4 Ligands: SO4.18 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.4, B:R.4 Salt bridges: B:R.4 SO4.18: 6 residues within 4Å: Chain A: D.119 Chain B: M.1, A.3, H.32, P.33 Ligands: SO4.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.32 Water bridges: B:R.4, B:R.4 Salt bridges: B:H.32

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

2018-04-25

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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