SMTL ID : 6vb1.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLU- LEU- ARG- ALA- ARG- GLU- GLU- ALA- TYR: Synthetic peptide GLU-LEU-ARG-ALA-ARG-GLU-GLU-ALA-TYR(Non-covalent)

GLU-LEU-ARG-ALA-ARG-GLU-GLU-ALA-TYR.1: 31 residues within 4Å: Chain A: Y.7, Y.9, M.45, Y.59, R.62, N.63, I.66, S.67, N.70, T.73, Y.74, E.76, S.77, N.80, L.81, Y.84, I.95, R.97, Y.99, S.116, Y.123, T.143, K.146, W.147, A.150, E.152, Q.155, L.156, Y.159, W.167, Y.171 41 PLIP interactions: 41 interactions with chain A Hydrophobic interactions: A:Y.7, A:I.66, A:I.66, A:T.73, A:Y.74, A:L.81, A:Y.123, A:Y.159, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:Y.9, A:N.63, A:N.63, A:Y.74, A:Y.74, A:S.77, A:N.80, A:R.97, A:Y.99, A:Y.99, A:S.116, A:T.143, A:K.146, A:E.152, A:Q.155, A:Y.159, A:Y.171 Water bridges: A:N.70, A:Y.74, A:R.97, A:D.114, A:E.152, A:E.152, A:E.152, A:Q.155 Salt bridges: A:R.62, A:R.97, A:K.146, A:E.152 pi-Stacking: A:W.147

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

EDO.2: 4 residues within 4Å: Chain A: E.264, G.265, L.266, P.267 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.264 EDO.3: 5 residues within 4Å: Chain A: R.6, F.8, M.98 Chain B: K.58 Ligands: GOL.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.6 Water bridges: B:F.56, B:K.58 EDO.6: 7 residues within 4Å: Chain A: L.206, R.234, Q.242 Chain B: Y.10, S.11, H.13, P.14 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.11, A:R.234, A:Q.242 Water bridges: A:Q.242

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.63 Ligands: EDO.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.30, B:Y.63 Water bridges: A:S.4, A:D.29

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

NA.5: 3 residues within 4Å: Chain B: N.83, H.84, L.87 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.83, B:H.84, B:H.84, B:L.87

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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