SMTL ID : 4zfz.1 (3 other biounits)

Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with myristoylated 5-mer lipopeptide derived from SIV Nef protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLY- GLY- ALA- ILE- SER: 5-mer lipopeptide from Protein Nef(Non-covalent)

GLY-GLY-ALA-ILE-SER.1: 13 residues within 4Å: Chain A: D.70, T.74, V.77, S.78, N.81, L.82, Y.85, Q.117, T.144, K.147, W.148, V.153 Ligands: MYR.26 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.74, A:V.153 Hydrogen bonds: A:S.78, A:S.78, A:N.81, A:Q.117, A:Q.117, A:T.144 Water bridges: A:W.148 Salt bridges: A:K.147

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: H.192, A.200, E.255 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.192, A:E.255 ZN.3: 2 residues within 4Å: Chain A: E.59, E.62 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.59, A:E.59, A:E.62 ZN.4: 2 residues within 4Å: Chain A: H.193 Chain B: D.99 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.99, A:H.193 ZN.5: 3 residues within 4Å: Chain A: A.1, H.4, Q.181 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.1, A:H.4 ZN.17: 2 residues within 4Å: Chain B: H.52 Ligands: EDO.25 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.52, H2O.9 ZN.18: 2 residues within 4Å: Chain B: E.37 Ligands: EDO.24 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.37, B:E.37, H2O.7

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

EDO.6: 9 residues within 4Å: Chain A: A.1, H.4, D.30, L.180, Q.181, Y.210, P.211, E.265 Ligands: TRS.15 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: G.2, L.104, G.105, P.106 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: M.6, Y.8, Q.64, Y.160, E.164, S.168, Y.172 Ligands: MYR.26 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: F.9, Y.28, D.30, D.31 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: R.36, E.47, P.48, R.49 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: R.109, L.110, E.162, L.166 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: G.238 Chain B: S.53, L.66, Y.68 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: R.7, M.99, Y.114 Chain B: K.59 Ligands: EDO.19 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: R.15, P.16, G.17, R.18, G.19 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: F.9, M.99, Q.116 Chain B: F.57, S.58, K.59, W.61 Ligands: EDO.13 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: R.22, I.24 Chain B: S.34, D.35 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: Q.9, V.10, K.95, W.96, D.97 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: W.205 Chain B: P.15, P.16, M.100 Ligands: EDO.23 Ligand excluded by PLIP EDO.23: 10 residues within 4Å: Chain A: W.205, L.207, R.235, Q.243 Chain B: Y.11, S.12, R.13, H.14, P.15 Ligands: EDO.22 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: E.37, N.84 Ligands: ZN.18 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: R.22, D.38 Chain B: H.52 Ligands: ZN.17 Ligand excluded by PLIP

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.15: 8 residues within 4Å: Chain A: A.1, S.3, H.4, S.5, D.30, P.211, E.265 Ligands: EDO.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.3, A:S.5, A:D.31 Water bridges: A:S.3, A:A.212

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 4 residues within 4Å: Chain A: F.37, S.39, A.72, R.76 Ligand excluded by PLIP

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.26: 11 residues within 4Å: Chain A: Y.8, V.25, Q.64, R.67, A.71, F.75, Y.115, W.157, Y.160 Ligands: GLY-GLY-ALA-ILE-SER.1, EDO.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.8, A:Y.8, A:V.25, A:A.71, A:W.157, A:Y.160 Water bridges: A:Q.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morita, D. et al., Crystal structure of the N-myristoylated lipopeptide-bound MHC class I complex. Nat Commun (2016)

Release Date

2016-01-13

Peptides

Major histocompatibility complex class I: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Major histocompatibility complex class I

Beta-2-microglobulin

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