SMTL ID : 6iwg.1

Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with N-myristoylated 4-mer lipopeptide derived from SIV nef protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MYR- GLY- GLY- ALA- ILE: N-myristoylated 4-mer lipopeptide(Non-covalent)

MYR-GLY-GLY-ALA-ILE.1: 20 residues within 4Å: Chain A: Y.24, V.34, R.35, F.36, T.45, A.67, R.70, T.73, D.77, T.80, L.81, Y.84, W.97, H.114, Y.123, T.143, K.146, W.147, Y.152 Ligands: EDO.8 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.34, A:T.45, A:D.77, A:L.81, A:W.97, A:W.97, A:Y.123, A:W.147 Hydrogen bonds: A:R.70, A:R.70, A:D.77, A:D.77, A:D.77, A:T.80, A:Y.84, A:K.146 Water bridges: A:D.77, A:Y.152, A:Y.152 Salt bridges: A:K.146

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

NA.2: 3 residues within 4Å: Chain A: Q.262, H.263, L.266 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.263, A:H.263 Water bridges: A:Q.262 NA.3: 2 residues within 4Å: Chain A: E.264 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.264 Water bridges: A:S.2 NA.4: 2 residues within 4Å: Chain A: D.183 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.183 NA.16: 2 residues within 4Å: Chain B: H.85, L.88 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.85, B:L.88, B:L.88, B:G.90

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

EDO.5: 7 residues within 4Å: Chain A: L.5, Y.7, R.66, Y.159, W.167, Y.171 Ligands: EDO.8 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: E.161 Ligands: BO3.15 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: D.122, Y.123, I.124, A.125, I.134, A.135, A.136 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: Y.7, E.63, R.66, Y.159 Ligands: MYR-GLY-GLY-ALA-ILE.1, EDO.5 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: S.88, E.89 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: D.30, P.235, G.239, F.241 Ligands: EDO.21 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: L.179, Q.180, H.181, P.210, E.264 Ligands: NA.3 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: F.8, Y.27, D.29 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: E.166, W.167, R.170 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: T.178, D.183, Y.209, G.239 Ligands: NA.4 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: K.7, I.8, R.92, V.94 Ligands: BO3.26 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: T.5, K.7, S.29, G.30 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: I.23 Chain B: S.34, D.35, L.55 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain A: W.204 Chain B: Y.11, S.12, P.16, W.96, D.97, R.98, M.100 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: G.237 Chain B: S.53, L.66, Y.68 Ligands: EDO.10 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: E.232, T.233 Chain B: Y.27, S.29 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: F.8 Chain B: F.57, S.58, K.59 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: K.42, M.47, E.70, F.71, T.72, Y.79 Ligand excluded by PLIP

3 x BO3: BORIC ACID(Non-functional Binders)(Non-covalent)

BO3.15: 1 residues within 4Å: Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.131, A:R.157, A:R.157, A:E.161 BO3.25: 3 residues within 4Å: Chain B: S.58, K.59, D.60 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.59, B:D.60 Water bridges: B:S.58, B:D.60, B:S.62, B:S.62 BO3.26: 3 residues within 4Å: Chain B: R.92, T.93 Ligands: EDO.17 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamamoto, Y. et al., Identification and Structure of an MHC Class I-Encoded Protein with the Potential to PresentN-Myristoylated 4-mer Peptides to T Cells. J Immunol. (2019)

Release Date

2019-08-14

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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