SMTL ID : 7wj2.1

Crystal structure of HLA-C*1402 complexed with 8-mer HIV gag peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

hetero-1-1-mer

Ligands

1 x LEU- TYR- ASN- THR- VAL- ALA- THR- LEU: 8-mer peptide(Non-covalent)

LEU-TYR-ASN-THR-VAL-ALA-THR-LEU.1: 26 residues within 4Å: Chain A: M.6, Y.8, S.10, F.23, E.64, K.67, Y.68, R.70, Q.71, T.74, S.78, N.81, Y.85, L.96, W.98, F.100, Y.124, T.144, K.147, W.148, E.153, R.157, Y.160, T.164, W.168, Y.172 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:Y.8, A:Y.68, A:Y.68, A:Q.71, A:T.74, A:L.96, A:W.98, A:W.98, A:F.100, A:F.100, A:Y.124, A:W.148, A:Y.160, A:T.164, A:W.168, A:W.168 Hydrogen bonds: A:S.10, A:S.10, A:E.64, A:Q.71, A:Q.71, A:S.78, A:N.81, A:Y.85, A:K.147, A:K.147, A:E.153, A:R.157, A:Y.172, A:Y.172 Water bridges: A:Y.8, A:Q.156 Salt bridges: A:K.147

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

EDO.2: 4 residues within 4Å: Chain A: N.128, W.134, T.135, Q.145 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.128, A:Q.145 Water bridges: A:A.136 EDO.3: 5 residues within 4Å: Chain A: F.9, Y.28, D.30, D.31 Chain B: Y.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.31 Water bridges: A:R.7 EDO.4: 4 residues within 4Å: Chain A: R.36, E.47, P.48, R.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.49 EDO.6: 9 residues within 4Å: Chain B: Y.11, S.12, P.15, A.16, W.96, D.97, R.98, M.100 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.12, B:A.16 EDO.7: 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.6 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.235, B:S.12, B:H.14, B:M.100 EDO.8: 6 residues within 4Å: Chain B: Q.9, V.10, K.95, W.96, D.97, M.100 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.10, B:K.95, B:D.97 Water bridges: B:I.8, B:M.100 EDO.9: 5 residues within 4Å: Chain A: V.13, S.93 Chain B: P.33, S.34, D.35 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.34, B:D.35, B:D.35 Water bridges: A:S.93

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

NA.5: 3 residues within 4Å: Chain A: V.232, E.233 Chain B: Q.9 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.9 Hydrogen bonds: A:E.233

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

ACT.10: 5 residues within 4Å: Chain B: I.36, E.37, N.84, H.85, V.86 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.37 Water bridges: B:V.86, B:V.86

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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