SMTL ID : 6vb5.1

HLA-B*15:02 complexed with a synthetic peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

1 x THR- VAL- ARG- ALA- SER- GLY- HIS- SER- TYR: Synthetic peptide THR-VAL-ARG-ALA-SER-GLY-HIS-SER-TYR(Non-covalent)

THR-VAL-ARG-ALA-SER-GLY-HIS-SER-TYR.1: 31 residues within 4Å: Chain A: Y.7, Y.9, M.45, Y.59, R.62, N.63, I.66, T.69, N.70, T.73, Y.74, E.76, S.77, N.80, L.81, Y.84, R.97, Y.99, D.114, S.116, Y.123, T.143, K.146, W.147, A.150, E.152, L.156, Y.159, W.167, Y.171 Ligands: ACT.8 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:Y.7, A:I.66, A:Y.74, A:L.81, A:Y.99, A:Y.123, A:E.152, A:Y.159, A:Y.159, A:W.167 Hydrogen bonds: A:R.62, A:R.62, A:N.63, A:N.63, A:N.63, A:T.73, A:T.73, A:Y.74, A:E.76, A:S.77, A:N.80, A:Y.84, A:R.97, A:Y.99, A:S.116, A:S.116, A:E.152, A:Y.171, A:Y.171 Water bridges: A:Y.99, A:Y.99, A:D.114, A:K.146 Salt bridges: A:D.114, A:K.146 pi-Stacking: A:W.147 pi-Cation interactions: A:Y.99

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

ACT.2: 6 residues within 4Å: Chain A: W.204, R.234, Q.242 Chain B: S.12, H.14, P.15 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.242, B:S.12, B:S.12 Water bridges: A:R.234 Salt bridges: A:R.234 Hydrophobic interactions: B:P.15 ACT.8: 9 residues within 4Å: Chain A: Y.9, N.70, T.73, Y.74, R.97 Ligands: THR-VAL-ARG-ALA-SER-GLY-HIS-SER-TYR.1, THR-VAL-ARG-ALA-SER-GLY-HIS-SER-TYR.1, THR-VAL-ARG-ALA-SER-GLY-HIS-SER-TYR.1, THR-VAL-ARG-ALA-SER-GLY-HIS-SER-TYR.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.73, A:Y.74 Water bridges: A:N.70, A:Y.99 Salt bridges: A:R.97

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.64 Ligands: EDO.6 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.30, B:Y.64

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

EDO.4: 4 residues within 4Å: Chain A: R.44, W.60, D.61, T.64 3 PLIP interactions: 3 interactions with chain A Water bridges: A:P.43, A:R.44, A:R.44 EDO.5: 1 residues within 4Å: Chain A: D.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.39 Water bridges: A:D.39 EDO.6: 4 residues within 4Å: Chain A: A.211, T.233, F.241 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.233

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

NA.7: 3 residues within 4Å: Chain B: N.84, H.85, L.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.88 Water bridges: B:N.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schutte, R.J. et al., HLA-B*15:02 complexed with a synthetic peptide. To Be Published

Release Date

2020-11-25

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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