SMTL ID : 5wki.1

Crystal structure of PG90 TCR-CD1b-PG complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- FUC- NAG- FUC: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG-FUC.1: 5 residues within 4Å: Chain A: N.56, F.57, P.166, R.167, L.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.170

1 x CUY: tetracosyl octadecanoate(Non-covalent)

CUY.2: 18 residues within 4Å: Chain A: V.11, I.12, Q.13, G.27, S.28, H.37, G.38, W.39, F.69, Y.72, I.73, F.76, I.95, G.97, A.99, L.113, F.143 Ligands: D3D.17 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.11, A:V.11, A:Q.13, A:H.37, A:F.69, A:F.69, A:F.69, A:I.73, A:F.76, A:I.95, A:A.99, A:F.143

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

NAG.3: 3 residues within 4Å: Chain A: T.18, N.19, T.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.18, A:N.19

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

EDO.4: 5 residues within 4Å: Chain A: W.189, S.191, H.206, R.245 Chain B: D.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.189 EDO.5: 1 residues within 4Å: Chain A: Y.162 No protein-ligand interaction detected (PLIP) EDO.6: 8 residues within 4Å: Chain A: H.10, I.12, W.30, D.32, I.98 Chain B: S.55, F.56, Y.63 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.55 Water bridges: B:S.57, A:D.32 EDO.7: 2 residues within 4Å: Chain A: G.199, R.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.199 EDO.8: 3 residues within 4Å: Chain A: D.40, D.42, S.43 No protein-ligand interaction detected (PLIP) EDO.9: 1 residues within 4Å: Chain B: H.51 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain C: K.3, T.26, E.31 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.3, C:E.31 EDO.11: 5 residues within 4Å: Chain C: S.131, N.177, K.178, S.179, F.181 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.177 EDO.12: 5 residues within 4Å: Chain C: N.57, E.58, A.60, S.61, P.76 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.60 EDO.13: 4 residues within 4Å: Chain C: K.130, S.131, W.175, S.176 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.131, C:S.176 Water bridges: C:S.176 EDO.14: 6 residues within 4Å: Chain C: M.10, D.11, C.12, A.17, A.18, N.19 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.19, C:N.19, C:N.19 EDO.15: 2 residues within 4Å: Chain C: P.76, H.77 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.16: 2 residues within 4Å: Chain C: A.184, F.198 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.184 NA.20: 3 residues within 4Å: Chain D: G.3, D.24, P.25 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.25

1 x D3D: (19S,22R,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9E)-octadec-9-enoate(Non-covalent)

D3D.17: 28 residues within 4Å: Chain A: L.65, I.68, V.71, Y.72, G.75, F.76, A.99, L.113, V.125, I.147, G.152, I.153, M.154, T.156, V.157, L.160, L.161, Y.168 Chain C: Y.32, R.91, A.93, Y.94, Q.96 Chain D: A.97, R.98, A.99, Q.100 Ligands: CUY.2 21 PLIP interactions: 16 interactions with chain A, 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: A:L.65, A:I.68, A:Y.72, A:Y.72, A:A.99, A:L.113, A:V.125, A:I.147, A:T.156, A:V.157, A:V.157, A:L.160, A:L.160, A:L.161, A:Y.168 Hydrogen bonds: A:I.153, C:Y.32, C:A.93, C:Q.96, D:A.97, D:Q.100

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

ACT.18: 2 residues within 4Å: Chain D: E.170, H.172 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.170 Salt bridges: D:H.172 ACT.19: 2 residues within 4Å: Chain D: Q.41, E.44 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.41, D:Q.41

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

CL.21: 2 residues within 4Å: Chain D: R.9, Y.220 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shahine, A. et al., A molecular basis of human T cell receptor autoreactivity toward self-phospholipids. Sci Immunol (2017)

Release Date

2017-11-01

Peptides

T-cell surface glycoprotein CD1b: A
Beta-2-microglobulin: B
T-cell receptor alpha variable 26-1,TRA@ protein: C
PG90 TCR beta chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

T-cell surface glycoprotein CD1b

Beta-2-microglobulin

T-cell receptor alpha variable 26-1,TRA@ protein

PG90 TCR beta chain

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