SMTL ID : 6vb2.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

hetero-1-1-mer

Ligands

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

GLU-LEU-ARG-ALA-ARG-GLN-GLU-CYS-TYR.1: 30 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, E.152, Q.155, L.156, Y.159, W.167, Y.171 40 PLIP interactions: 40 interactions with chain A Hydrophobic interactions: A:Y.7, A:I.66, 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:Y.59, A:N.63, A:N.63, A:Y.74, 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:Q.155, A:Y.159, A:Y.171 Water bridges: A:N.70, A:R.97, A:D.114, A:K.146, A:E.152, A:E.152, A:E.152 Salt bridges: A:R.62, A:K.146, A:E.152 pi-Stacking: A:W.147

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

NA.2: 2 residues within 4Å: Chain A: Q.180, E.264 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.180

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.62 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.62 Water bridges: B:Y.62, A:R.6 GOL.10: 8 residues within 4Å: Chain B: I.6, Q.7, V.8, V.92, K.93, W.94, D.95 Ligands: ACT.4 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:R.234, B:Q.7 Hydrogen bonds: B:V.8, B:K.93, B:D.95

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

ACT.4: 8 residues within 4Å: Chain A: W.204, R.234, W.244 Chain B: V.8, Y.9, D.95 Ligands: GOL.10, ACT.11 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:W.244, B:S.10 Salt bridges: A:R.234 ACT.11: 9 residues within 4Å: Chain A: W.204, R.234, Q.242 Chain B: Y.9, S.10, R.11, H.12, P.13 Ligands: ACT.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.234 Hydrogen bonds: B:S.10 Water bridges: B:S.10

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

EDO.5: 3 residues within 4Å: Chain A: R.145, K.146, A.149 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: G.252, E.253, R.256 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.252, A:Q.255 EDO.7: 3 residues within 4Å: Chain A: N.127, E.128, D.129 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.128, A:D.129, A:D.129 Water bridges: A:E.128 EDO.8: 2 residues within 4Å: Chain A: H.188, W.204 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.188 Water bridges: B:R.96 EDO.9: 3 residues within 4Å: Chain A: S.92, H.93, D.119 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Water bridges: B:Q.1, B:Q.1, B:Q.1, B:H.30, A:Q.87, A:Q.87, A:H.93, A:D.119, A:D.119 Hydrogen bonds: A:H.93

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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