SMTL ID : 6iwh.1

Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with C14-GGGI lipopeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MYR- GLY- GLY- GLY- ILE: C14-GGGI lipopeptide(Non-covalent)

MYR-GLY-GLY-GLY-ILE.1: 24 residues within 4Å: Chain A: Y.7, Y.24, V.34, R.35, F.36, T.45, E.63, A.67, R.70, T.73, D.77, T.80, L.81, Y.84, L.95, W.97, A.99, H.114, Y.123, T.143, K.146, W.147, Y.152 Ligands: EDO.9 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:Y.7, A:Y.24, A:V.34, A:F.36, A:T.45, A:D.77, A:L.81, A:Y.84, A:L.95, A:W.97, A:W.97, A:W.97, A:A.99, A:Y.123, A:W.147 Hydrogen bonds: A:R.70, A:R.70, A:D.77, A:Y.84, A:K.146, A:Y.152 Water bridges: A:D.77, A:D.77, A:D.77, A:W.147, A:W.147, A:Y.152, A:Y.152 Salt bridges: A:K.146

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

NA.2: 3 residues within 4Å: Chain A: Q.262, H.263, L.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.263, A:H.263 NA.3: 3 residues within 4Å: Chain A: G.1, E.264 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) NA.4: 5 residues within 4Å: Chain A: T.178, H.181, D.183, Y.209 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.178 NA.11: 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 Water bridges: B:G.90 NA.12: 2 residues within 4Å: Chain B: I.36, Y.67 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.36 Water bridges: B:I.36

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

EDO.5: 6 residues within 4Å: Chain A: L.5, Y.7, Y.159, W.167, Y.171 Ligands: EDO.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.7, A:R.66, A:Y.159, A:Y.159, A:Y.171 EDO.6: 8 residues within 4Å: Chain A: L.179, Q.180, H.181, A.182, Y.209, P.210, E.264 Ligands: NA.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.180 EDO.7: 7 residues within 4Å: Chain A: D.122, Y.123, I.124, A.125, I.134, A.135, A.136 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.122, A:D.122, A:D.122, A:Y.123 EDO.8: 6 residues within 4Å: Chain A: T.178, D.183, Y.209, G.239, T.240 Ligands: NA.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.178, A:T.178 EDO.9: 6 residues within 4Å: Chain A: Y.7, E.63, R.66, Y.159 Ligands: MYR-GLY-GLY-GLY-ILE.1, EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.63, A:R.66 EDO.10: 4 residues within 4Å: Chain A: I.213, T.214, L.215, K.243 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.215, A:L.215, A:K.243 Water bridges: A:I.213, A:I.213, A:I.213 EDO.13: 6 residues within 4Å: Chain A: M.98, Q.115 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.115 EDO.14: 4 residues within 4Å: Chain B: K.7, I.8, V.94 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.8 Water bridges: B:R.92 EDO.15: 4 residues within 4Å: Chain B: R.92, T.93, V.94 Ligands: EDO.14 No protein-ligand interaction detected (PLIP) EDO.16: 4 residues within 4Å: Chain B: T.87, L.88, S.89, R.92 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.89, B:R.92 EDO.17: 5 residues within 4Å: Chain A: V.12, S.92 Chain B: P.33, S.34, D.35 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.34, B:D.35, B:D.35, A:S.92, A:S.92 EDO.18: 4 residues within 4Å: Chain A: R.21, I.23 Chain B: S.34, D.35 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.35 EDO.19: 5 residues within 4Å: Chain B: R.4, T.5, K.7, S.29, G.30 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.7, B:K.7 Water bridges: B:R.4, B:S.62, B:S.62

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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