SMTL ID : 4elk.1 (1 other biounit)

Crystal structure of the Hy19.3 type II NKT TCR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 2 residues within 4Å: Chain A: R.61, Q.81 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.61 Water bridges: A:R.61, A:R.61 Salt bridges: A:R.61 ACT.2: 9 residues within 4Å: Chain A: K.134, S.135, V.136, W.179, N.181 Chain B: F.129, L.147, T.149 Ligands: FMT.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.135 Water bridges: A:S.180 Hydrophobic interactions: B:L.147 ACT.4: 9 residues within 4Å: Chain A: Q.39, S.41, G.42, L.87, R.109 Chain B: Q.38, G.41, F.92, Q.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.41, A:G.42 ACT.6: 5 residues within 4Å: Chain B: G.17, Q.18, M.19, Q.81, P.82 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.18 ACT.7: 3 residues within 4Å: Chain B: P.3, K.4, L.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.4

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 6 residues within 4Å: Chain A: Y.157, W.179 Chain B: T.149, E.180, S.190 Ligands: ACT.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.179, B:S.190 FMT.8: 2 residues within 4Å: Chain B: S.74, Y.75 No protein-ligand interaction detected (PLIP) FMT.9: 5 residues within 4Å: Chain B: S.88, A.89, R.111, L.112, T.113 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.89, B:R.111, B:R.111, B:T.113 FMT.10: 2 residues within 4Å: Chain B: S.198, F.201 No protein-ligand interaction detected (PLIP)

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.5: 7 residues within 4Å: Chain A: W.35, K.46, A.47, L.48, M.49, E.59 Chain B: E.103 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:E.103, A:L.48 Water bridges: A:K.46, A:S.50 Salt bridges: A:K.46, A:K.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Girardi, E. et al., Type II natural killer T cells use features of both innate-like and conventional T cells to recognize sulfatide self antigens. Nat.Immunol. (2012)

Release Date

2012-07-25

Peptides

Hy19.3 TCR alpha chain (mouse variable domain, human constant domain): A
Hy19.3 TCR beta chain (mouse variable domain, human constant domain): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hy19.3 TCR alpha chain (mouse variable domain, human constant domain)

Hy19.3 TCR beta chain (mouse variable domain, human constant domain)

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