SMTL ID : 7ryo.1

CD1a-dideoxymycobactin-gdTCR complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: G.235, D.236, R.248 Chain B: Q.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.236, A:D.236 EDO.2: 4 residues within 4Å: Chain A: Q.227, E.228, Q.229, Q.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.227, A:Q.229, A:Q.230

1 x WGR: dideoxymycobactin-838(Non-covalent)

WGR.3: 29 residues within 4Å: Chain A: F.12, V.14, W.16, V.30, S.31, G.32, H.40, I.49, W.65, F.72, R.75, S.79, I.83, Y.86, F.92, I.98, V.100, G.102, L.116, L.118, F.125, W.133, F.146, L.150, E.156, L.163, L.164, T.167, C.168 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.12, A:V.14, A:W.16, A:W.16, A:V.30, A:H.40, A:I.49, A:W.65, A:F.72, A:Y.86, A:F.92, A:I.98, A:V.100, A:L.116, A:L.118, A:F.125, A:W.133, A:L.150, A:L.164 pi-Stacking: A:F.146

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain C: Q.179 Chain D: L.41, P.42 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wegrecki, M. et al., Atypical sideways recognition of CD1a by autoreactive gamma delta T cell receptors. Nat Commun (2022)

Release Date

2022-05-18

Peptides

T-cell surface glycoprotein CD1a: A
Beta-2-microglobulin: B
T cell receptor gamma variable 4,T cell receptor beta constant 1: C
T cell receptor delta variable 1,T cell receptor alpha chain constant: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

T-cell surface glycoprotein CD1a

Beta-2-microglobulin

T cell receptor gamma variable 4,T cell receptor beta constant 1

T cell receptor delta variable 1,T cell receptor alpha chain constant

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