SMTL ID : 6z9v.1 (1 other biounit)

Human Class I Major Histocompatibility Complex, A02 allele, presenting IIGWMWIPV

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ILE- ILE- GLY- TRP- MET- TRP- ILE- PRO- VAL: ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL(Non-covalent)

ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL.1: 29 residues within 4Å: Chain A: Y.7, M.45, Y.59, E.63, K.66, V.67, A.69, H.70, T.73, D.77, T.80, L.81, Y.84, R.97, Y.99, H.114, Y.116, T.143, K.146, W.147, V.152, Q.155, Y.159, T.163, W.167, Y.171 Ligands: EDO.3, EDO.11, P4G.12 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:Y.7, A:Y.59, A:K.66, A:K.66, A:V.67, A:T.73, A:D.77, A:L.81, A:Y.99, A:Y.116, A:T.143, A:W.147, A:V.152, A:T.163, A:W.167, A:W.167 Hydrogen bonds: A:E.63, A:H.70, A:D.77, A:Y.99, A:T.143, A:K.146, A:Y.159, A:Y.171 Water bridges: A:T.73, A:D.77, A:R.97, A:Y.99 Salt bridges: A:K.146 pi-Stacking: A:H.70 pi-Cation interactions: A:H.70

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

EDO.2: 7 residues within 4Å: Chain A: H.263, E.264, L.266, P.267, K.268, P.269 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.264, A:K.268 EDO.3: 4 residues within 4Å: Chain A: G.62, R.65, K.66 Ligands: ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.65, A:R.65 EDO.9: 7 residues within 4Å: Chain B: Q.9, V.10, V.94, K.95, W.96, D.97, M.100 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.10, B:D.97, B:D.97 Water bridges: B:I.8, B:M.100 EDO.10: 9 residues within 4Å: Chain A: W.204, L.206, R.234, Q.242 Chain B: Y.11, S.12, H.14, P.15, M.100 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.12, B:M.100, A:R.234 Water bridges: A:Q.242 EDO.11: 6 residues within 4Å: Chain A: R.97, W.147, V.152 Ligands: ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL.1, ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL.1, ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.97, A:R.97

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: T.190, H.191, H.192, T.200, L.201, R.202 Chain B: D.99 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.192, A:T.200, A:R.202, A:R.202 Water bridges: A:T.190

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

SO4.5: 3 residues within 4Å: Chain A: E.166, W.167, R.170 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.170, A:R.170, A:R.170 SO4.6: 5 residues within 4Å: Chain A: F.8, Y.27, D.29, D.30 Chain B: Y.64 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.64, A:D.29 SO4.7: 5 residues within 4Å: Chain A: E.264, G.265, L.266, P.267 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.265

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 3 residues within 4Å: Chain B: N.84, H.85, L.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.84, B:H.85, B:L.88

1 x P4G: 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE(Non-covalent)

P4G.12: 9 residues within 4Å: Chain A: Q.155, L.156, Y.159, T.163 Ligands: ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL.1, ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL.1, ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL.1, ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL.1, ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.156 Hydrogen bonds: A:K.66 Water bridges: A:T.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Man, S. et al., Synthetic Peptides with Inadvertent Chemical Modifications Can Activate Potentially Autoreactive T Cells. J Immunol. (2021)

Release Date

2021-06-30

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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