SMTL ID : 7wt3.2 (1 other biounit)

Crystal structure of HLA-A*2402 complexed with 4-mer lipopeptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MYR- GLY- ALA- ASN- PHE: 4-mer lipopeptide(Non-covalent)

MYR-GLY-ALA-ASN-PHE.1: 22 residues within 4Å: Chain A: Y.8, A.25, V.26, V.35, R.36, F.37, K.67, V.68, H.71, T.74, E.77, N.78, I.81, Y.85, L.96, F.100, Y.117, Y.124, T.144, K.147, W.148, Q.157 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.8, A:A.25, A:V.35, A:V.68, A:N.78, A:I.81, A:L.96, A:F.100, A:T.144, A:W.148 Hydrogen bonds: A:E.77, A:N.78, A:N.78, A:Y.85, A:Q.157 Water bridges: A:T.74 Salt bridges: A:K.147 pi-Stacking: A:Y.117, A:Y.124

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

ACT.2: 6 residues within 4Å: Chain A: S.10, T.11, I.24, V.26 Chain B: L.55, F.57 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.55 Hydrogen bonds: A:T.11, A:T.11

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: A.1, H.4, Q.181 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.1, A:H.4, H2O.2

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

EDO.4: 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.5: 7 residues within 4Å: Chain A: R.15, E.20, P.21, R.22, S.39, D.40, R.76 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.15, A:R.15, A:E.20, A:S.39, A:D.40, A:R.76 EDO.6: 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.7: 6 residues within 4Å: Chain A: F.110, E.129, D.130, L.131, R.132, E.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.132 Water bridges: A:L.111 EDO.8: 7 residues within 4Å: Chain A: R.36, F.37, D.38, A.41, S.43, R.45, E.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.38, A:R.45 Water bridges: A:A.41 EDO.9: 5 residues within 4Å: Chain A: M.6, Y.8, Y.160, T.164, Y.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.8, A:Y.160, A:Y.172 EDO.10: 5 residues within 4Å: Chain A: I.24, R.36, D.38 Chain B: D.54, L.55 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.36, B:L.55 Water bridges: A:R.22 EDO.11: 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.12: 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.13: 4 residues within 4Å: Chain A: R.132, E.149, H.152, A.154 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.132, A:E.149, A:H.152 Water bridges: A:A.154 EDO.14: 7 residues within 4Å: Chain A: F.9, M.99, Q.116 Chain B: F.57, S.58, K.59, W.61 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.116, B:S.58

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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