SMTL ID : 7byd.1 (1 other biounit)

Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*05104

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x GLY- GLY- ALA- ILE: GLY-GLY-ALA-ILE(Non-covalent)

GLY-GLY-ALA-ILE.1: 14 residues within 4Å: Chain A: T.73, D.77, L.81, Y.84, Y.123, T.143, K.146, W.147, Y.152 Chain D: D.96, A.99, E.101, Y.103 Ligands: MYR.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.81, A:Y.84 Hydrogen bonds: A:D.77, A:T.143, A:Y.152, A:Y.152, A:Y.152 Salt bridges: A:K.146

9 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.3: 4 residues within 4Å: Chain A: R.48, A.49, P.50, E.53 Ligand excluded by PLIP IOD.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: R.14, E.19, P.20 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain B: N.18, P.73, R.98 Ligand excluded by PLIP IOD.8: 5 residues within 4Å: Chain B: G.44, E.78, Y.79, A.80, K.95 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain C: F.45, I.47, Q.48, N.56 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain D: Q.215, T.234, Q.235 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain C: S.148 Chain D: Q.182, A.184 Ligand excluded by PLIP

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

EDO.6: 5 residues within 4Å: Chain A: F.8, Y.27, D.29, D.30 Chain B: Y.64 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.64

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

TRS.9: 4 residues within 4Å: Chain A: G.237 Chain B: S.53, L.66, Y.68 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.68

1 x CA: CALCIUM ION(Non-covalent)

CA.10: 2 residues within 4Å: Chain B: H.85, L.88 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.85, B:L.88, H2O.1

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.11: 16 residues within 4Å: Chain A: Y.7, Y.24, V.25, V.34, F.36, T.45, R.66, A.67, R.70, W.97, A.99, Y.152 Chain D: A.99, E.101 Ligands: GLY-GLY-ALA-ILE.1, GLY-GLY-ALA-ILE.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.7, A:V.34, A:F.36, A:T.45, A:A.67, A:W.97, A:W.97, A:A.99 Hydrogen bonds: A:R.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morita, D. et al., Crystal structure of the ternary complex of TCR, MHC class I and lipopeptides. Int.Immunol. (2020)

Release Date

2021-03-31

Peptides

B protein: A
Beta-2-microglobulin: B
SN45 T cell receptor alpha chain: C
SN45 T cell receptor beta chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

B protein

Beta-2-microglobulin

SN45 T cell receptor alpha chain

SN45 T cell receptor beta chain

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