SMTL ID : 7wt4.2 (1 other biounit)

Crystal structure of HLA-A*2402 complexed with 8-mer Influenza PB1 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ARG- TYR- GLY- PHE- VAL- ALA- ASN- PHE: PB1 peptide(Non-covalent)

ARG-TYR-GLY-PHE-VAL-ALA-ASN-PHE.1: 32 residues within 4Å: Chain A: M.6, Y.8, A.25, M.46, Y.60, E.63, E.64, K.67, V.68, H.71, T.74, D.75, E.77, N.78, I.81, Y.85, L.96, M.98, F.100, H.115, Y.117, Y.124, T.144, K.147, W.148, Q.156, Q.157, Y.160, T.164, G.168, Y.172 Ligands: EDO.6 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:Y.8, A:K.67, A:V.68, A:H.71, A:T.74, A:N.78, A:I.81, A:L.96, A:Y.124, A:Y.124, A:Q.156, A:Y.160, A:T.164 Hydrogen bonds: A:Y.8, A:E.64, A:K.67, A:K.67, A:N.78, A:N.78, A:N.78, A:Y.85, A:Q.157, A:Y.172, A:Y.172 Water bridges: A:W.148 Salt bridges: A:E.63, A:E.64, A:K.147 pi-Stacking: A:F.100, A:Y.117

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

EDO.2: 3 residues within 4Å: Chain A: A.1, G.2, E.265 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.2, A:S.3 EDO.3: 6 residues within 4Å: Chain A: R.112, G.113, Y.114, L.127, K.128, E.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.112, A:G.113 Water bridges: A:G.113 EDO.4: 6 residues within 4Å: Chain A: F.110, E.129, D.130, L.131, E.162 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.162 EDO.5: 3 residues within 4Å: Chain A: R.45, M.46, W.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.45, A:M.46 EDO.6: 3 residues within 4Å: Chain A: A.70, T.74 Ligands: ARG-TYR-GLY-PHE-VAL-ALA-ASN-PHE.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.74 Water bridges: A:T.74 EDO.7: 4 residues within 4Å: Chain A: S.106, D.107, G.108, R.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.170 EDO.8: 4 residues within 4Å: Chain A: F.9, Y.28, D.30, D.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.31 Water bridges: A:D.30 EDO.9: 4 residues within 4Å: Chain A: E.149, H.152, A.154, E.155 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.149, A:E.155, A:E.155, A:E.155 Water bridges: A:R.158 EDO.10: 5 residues within 4Å: Chain A: F.37, S.39, Q.44, S.72, Q.73 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.39, A:Q.44, A:S.72, A:Q.73 EDO.11: 2 residues within 4Å: Chain A: F.110 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.110 EDO.12: 7 residues within 4Å: Chain A: R.36, F.37, D.38, A.41, S.43, R.45, E.47 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.36, A:D.38, A:R.45, A:R.45 Water bridges: A:R.36, A:A.41 EDO.14: 5 residues within 4Å: Chain A: I.24, D.38 Chain B: S.53, D.54, L.55 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.54, B:L.55 Water bridges: A:R.22, A:R.36, A:D.38 EDO.15: 6 residues within 4Å: Chain A: F.9, Q.116 Chain B: F.57, S.58, K.59, W.61 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:S.58 Hydrogen bonds: A:Q.116

1 x ZN: ZINC ION(Non-covalent)

ZN.13: 3 residues within 4Å: Chain A: A.1, H.4, Q.181 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.1, A:H.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Asa, M. et al., Crystal structures of N-myristoylated lipopeptide-bound HLA class I complexes indicate reorganization of B-pocket architecture upon ligand binding. J.Biol.Chem. (2022)

Release Date

2022-06-22

Peptides

MHC class I antigen: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

MHC class I antigen

Beta-2-microglobulin

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