SMTL ID : 7wj3.1

Crystal structure of HLA-C*1402 complexed with 4-mer lipopeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLY- ALA- ALA- LEU: 4-mer lipopeptide(Non-covalent)

GLY-ALA-ALA-LEU.1: 12 residues within 4Å: Chain A: T.74, V.77, S.78, N.81, Y.85, L.96, Y.124, T.144, K.147, W.148, E.153 Ligands: MYR.20 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.77, A:L.96, A:Y.124, A:W.148 Hydrogen bonds: A:S.78, A:N.81, A:Y.85, A:E.153 Salt bridges: A:K.147

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

EDO.2: 7 residues within 4Å: Chain A: D.123, Y.124, I.125, A.126, T.135, A.136, A.137 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: H.189, T.191, W.205, L.207 Chain B: R.98, D.99 Ligands: EDO.12 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: G.208, A.237, D.239, T.241, F.242, Q.243 Chain B: R.13, H.14 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: D.138, T.139 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: W.134, T.135, A.136, Q.142, Q.145 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: Y.8, E.64, K.67, F.100, Y.160 Ligands: EDO.8, MYR.20 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: M.6, Y.8, Y.160, W.168, Y.172 Ligands: EDO.7 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: Y.86, Y.119, K.122 Ligands: EDO.10 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: Y.86, Y.119, K.122, D.123, Y.124, D.138 Ligands: EDO.9 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: M.99, Q.116 Chain B: F.57, K.59, W.61 Ligand excluded by PLIP EDO.12: 10 residues within 4Å: Chain A: W.205, L.207, R.235, Q.243 Chain B: Y.11, S.12, H.14, P.15, M.100 Ligands: EDO.3 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: R.22, I.24 Chain B: S.34, D.35, L.55 Ligands: EDO.15 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: K.42, E.70, F.71, T.72 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: V.13, R.15, R.18, R.22 Chain B: D.35 Ligands: EDO.13 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain B: Q.9, V.10, V.94, K.95, W.96, D.97, M.100 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: G.121 Chain B: I.2, R.4, H.32, D.60, W.61, S.62 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: E.37, V.38, D.39, R.82, N.84, P.91 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: P.6, I.8, K.92 Ligand excluded by PLIP

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.20: 12 residues within 4Å: Chain A: Y.8, F.9, S.10, A.25, K.67, Y.68, R.70, Q.71, W.98, F.100 Ligands: GLY-ALA-ALA-LEU.1, EDO.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.8, A:A.25, A:K.67, A:Y.68, A:Y.68, A:R.70, A:Q.71, A:W.98, A:W.98, A:F.100, A:F.100

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 protein: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MHC class I protein

Beta-2-microglobulin

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