SMTL ID : 4zfz.4 (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 Compare

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: 12 residues within 4Å: Chain A: D.70, T.74, V.77, S.78, N.81, Y.85, Q.117, T.144, K.147, W.148, V.153 Ligands: MYR.25 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.74, A:V.153 Hydrogen bonds: A:T.74, A:S.78, A:N.81, A:Y.85, A:Q.117 Water bridges: A:S.78, A:S.78 Salt bridges: A:K.147

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: H.192, A.200, E.255 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.192, A:E.255, A:E.255 ZN.3: 4 residues within 4Å: Chain A: A.1, H.4 Ligands: EDO.11, EDO.15 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.1, A:H.4 ZN.17: 2 residues within 4Å: Chain A: H.193 Chain B: D.99 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.193, B:D.99 ZN.18: 2 residues within 4Å: Chain B: H.52 Ligands: EDO.24 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.52, H2O.7, H2O.8

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

EDO.4: 5 residues within 4Å: Chain A: F.9, Y.28, D.30, D.31 Chain B: Y.64 Ligand excluded by PLIP EDO.5: 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.6: 7 residues within 4Å: Chain A: G.208, D.239, T.241, F.242, Q.243 Chain B: R.13, H.14 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: W.205, R.235, W.245 Chain B: V.10, Y.11, D.97 Ligands: EDO.20, EDO.23 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: Y.86, Q.88, Y.119, D.120, R.122 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: M.6, Y.8, Q.64, Y.160, E.164, S.168, Y.172 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: A.1, S.3, D.30, P.211 Ligands: EDO.11 Ligand excluded by PLIP EDO.11: 10 residues within 4Å: Chain A: A.1, H.4, D.30, L.180, R.182, A.183, P.211, E.265 Ligands: ZN.3, EDO.10 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: A.137, D.138 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: Q.33, R.49 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: Q.116, D.123 Chain B: K.59, W.61 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: A.1, G.2, H.4, Q.181 Ligands: ZN.3 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: F.9, M.99 Chain B: F.57, S.58, K.59, W.61 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain A: L.207, R.235, Q.243 Chain B: Y.11, S.12, H.14, P.15, M.100 Ligands: EDO.7 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: R.22 Chain B: S.34, D.35, L.55 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: E.37, D.39, R.82, N.84, P.91 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: R.203, W.205, W.245 Chain B: D.97, D.99, M.100 Ligands: EDO.7 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: H.52, Y.67 Ligands: ZN.18 Ligand excluded by PLIP

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

CL.16: 2 residues within 4Å: Chain A: F.37, R.76 Ligand excluded by PLIP

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.25: 6 residues within 4Å: Chain A: Q.156, W.157, Y.160 Ligands: GLY-GLY-ALA-ILE-SER.1, GLY-GLY-ALA-ILE-SER.1, GLY-GLY-ALA-ILE-SER.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.156, A:W.157, A:W.157, A:Y.160

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
J

B
K

Major histocompatibility complex class I

Beta-2-microglobulin

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