SMTL ID : 7ryn.1

CD1a-sulfatide-gdTCR complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x CIS: (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE(Non-covalent)

CIS.1: 28 residues within 4Å: Chain A: F.12, V.14, W.16, G.32, H.40, I.49, W.65, L.68, F.72, R.75, T.76, R.78, S.79, I.83, R.85, V.100, G.102, W.133, F.146, L.150, Q.152, N.153, E.156, T.160, L.163, L.164, C.168, F.171 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:F.12, A:V.14, A:W.16, A:W.16, A:W.16, A:H.40, A:I.49, A:I.49, A:W.65, A:L.68, A:F.72, A:F.72, A:F.72, A:R.75, A:T.76, A:I.83, A:V.100, A:W.133, A:F.146, A:L.164, A:F.171 Hydrogen bonds: A:R.78, A:R.85, A:N.153 Salt bridges: A:R.78

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

EDO.2: 5 residues within 4Å: Chain A: Q.227, E.228, Q.229, Q.230, G.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.230, A:G.231 EDO.4: 3 residues within 4Å: Chain A: E.280, G.281, S.282 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.282 EDO.5: 4 residues within 4Å: Chain A: G.235, D.236, R.248 Chain B: Q.11 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.11, A:D.236, A:R.248, A:R.248 EDO.6: 4 residues within 4Å: Chain A: D.36, Y.214, K.216, W.245 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.216 EDO.7: 6 residues within 4Å: Chain A: S.240, A.241, D.242 Chain B: F.25, N.27, Y.70 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.241, A:D.242, A:D.242, B:N.27, B:N.27 EDO.10: 5 residues within 4Å: Chain B: H.16, S.23, N.24, F.25, E.72 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.16, B:E.72

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 3 residues within 4Å: Chain A: N.59, L.173, G.174 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 5 residues within 4Å: Chain A: Q.117, D.124 Chain B: K.61, D.62, W.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.117, A:Q.117

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

SO4.9: 4 residues within 4Å: Chain A: H.23, F.92, Y.94 Chain C: S.63 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.63, A:Y.94 Salt bridges: A:H.23 SO4.11: 3 residues within 4Å: Chain C: G.167, H.211, R.213 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.211, C:R.213

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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