SMTL ID : 5l2k.1 (1 other biounit)

Crystal structure of GEM42 TCR-CD1b-GMM complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: N.56, F.57, E.61, R.167, L.170, G.171 Ligands: SO4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.56, A:R.167 NAG.2: 4 residues within 4Å: Chain A: T.18, N.19, T.21, W.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.21 NAG.3: 1 residues within 4Å: Chain A: N.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.127

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

SO4.4: 2 residues within 4Å: Chain A: N.56 Ligands: NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.56 SO4.5: 5 residues within 4Å: Chain A: F.74, R.78 Chain D: E.30, K.71, R.96 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:E.30, D:E.30 Salt bridges: D:K.71, D:R.96, A:R.78 SO4.6: 4 residues within 4Å: Chain A: R.158, E.163 Chain C: F.29, R.66 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Salt bridges: C:R.66, A:R.158 SO4.13: 3 residues within 4Å: Chain C: P.7, T.8, E.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.8, C:E.9, C:E.9 SO4.15: 3 residues within 4Å: Chain D: Q.224, D.225, R.226 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.225

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

CL.7: 1 residues within 4Å: Chain A: S.138 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.139 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: T.7, L.103 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: K.41, F.70, T.71 Ligand excluded by PLIP

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

NA.10: 4 residues within 4Å: Chain A: Q.230, G.232, R.245, T.247 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.247 NA.16: 2 residues within 4Å: Chain D: H.166, S.167 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.166, D:S.167

1 x 6UL: TETRACOSYL PALMITATE(Non-covalent)

6UL.11: 18 residues within 4Å: Chain A: V.11, I.12, Q.13, S.28, W.39, A.46, F.69, Y.72, F.76, I.95, G.97, L.113, G.115, A.116, F.122, L.123, F.143 Ligands: 70E.17 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.11, A:Q.13, A:A.46, A:F.69, A:F.69, A:Y.72, A:F.76, A:L.113, A:F.122, A:F.143, A:F.143, A:F.143 Hydrogen bonds: A:A.116

1 x CS: CESIUM ION(Non-covalent)

CS.14: 2 residues within 4Å: Chain C: R.59, K.81 No protein-ligand interaction detected (PLIP)

1 x 70E: 6-O-[(2R,3R)-3-hydroxy-2-tetradecyldocosanoyl]-alpha-L-idopyranose(Non-covalent)

70E.17: 38 residues within 4Å: Chain A: F.9, V.11, H.37, L.65, F.69, V.71, Y.72, G.75, F.76, A.99, L.113, L.123, V.125, C.130, I.147, Y.150, G.152, I.153, M.154, V.157, L.160, L.161, C.165, Y.168 Chain C: N.30, Y.48, R.91, G.94, G.95, F.96 Chain D: Y.31, P.95, R.96, L.97, A.98, G.99, D.100 Ligands: 6UL.11 33 PLIP interactions: 21 interactions with chain A, 6 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: A:V.11, A:L.65, A:L.65, A:F.69, A:V.71, A:Y.72, A:Y.72, A:Y.72, A:F.76, A:L.113, A:L.123, A:V.125, A:I.147, A:I.147, A:V.157, A:L.161, A:Y.168, D:R.96, D:L.97 Hydrogen bonds: A:G.152, A:G.152, A:I.153, A:T.156, D:Y.31, D:A.98, D:G.99, D:D.100, C:N.30, C:Y.48, C:R.91, C:R.91, C:G.94 Salt bridges: C:R.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gras, S. et al., T cell receptor recognition of CD1b presenting a mycobacterial glycolipid. Nat Commun (2016)

Release Date

2016-11-16

Peptides

T-cell surface glycoprotein CD1b: A
Beta-2-microglobulin: B
GEM42 TCR alpha chain: C
GEM42 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

GEM42 TCR alpha chain

GEM42 TCR beta chain

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