SMTL ID : 5l2k.2 (1 other biounit)

Crystal structure of GEM42 TCR-CD1b-GMM complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-4-4-4-4-mer

Ligands

12 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: 5 residues within 4Å: Chain A: N.127 Chain D: N.127, A.128, R.158 Ligands: SO4.21 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.128 Hydrogen bonds: A:N.127 NAG.16: 7 residues within 4Å: Chain D: N.56, F.57, E.61, R.167, L.170, G.171 Ligands: SO4.19 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.56, D:R.167 NAG.17: 4 residues within 4Å: Chain D: T.18, N.19, T.21, W.22 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.21 NAG.18: 5 residues within 4Å: Chain A: N.127, A.128, R.158 Chain D: N.127 Ligands: SO4.6 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:A.128 Hydrogen bonds: D:N.127 NAG.31: 7 residues within 4Å: Chain G: N.56, F.57, E.61, R.167, L.170, G.171 Ligands: SO4.34 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.56, G:R.167 NAG.32: 4 residues within 4Å: Chain G: T.18, N.19, T.21, W.22 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:T.21, G:T.21 NAG.33: 5 residues within 4Å: Chain G: N.127 Chain J: N.127, A.128, R.158 Ligands: SO4.51 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain J Hydrogen bonds: G:N.127 Hydrophobic interactions: J:A.128 NAG.46: 7 residues within 4Å: Chain J: N.56, F.57, E.61, R.167, L.170, G.171 Ligands: SO4.49 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.56, J:R.167 NAG.47: 4 residues within 4Å: Chain J: T.18, N.19, T.21, W.22 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:T.21, J:T.21 NAG.48: 5 residues within 4Å: Chain G: N.127, A.128, R.158 Chain J: N.127 Ligands: SO4.36 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain J Hydrophobic interactions: G:A.128 Hydrogen bonds: J:N.127

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

SO4.4: 3 residues within 4Å: Chain A: N.56 Chain G: K.60 Ligands: NAG.1 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: F.74, R.78 Chain C: E.30, K.71, R.96 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: R.158, E.163 Ligands: NAG.18 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain C: Q.224, D.225, R.226 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain D: N.56 Chain J: K.60 Ligands: NAG.16 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain D: F.74, R.78 Chain F: E.30, K.71, R.96 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain D: R.158, E.163 Ligands: NAG.3 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain F: Q.224, D.225, R.226 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain A: K.60 Chain G: N.56 Ligands: NAG.31 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain G: F.74, R.78 Chain I: E.30, K.71, R.96 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain G: R.158, E.163 Ligands: NAG.48 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain I: Q.224, D.225, R.226 Ligand excluded by PLIP SO4.49: 3 residues within 4Å: Chain D: K.60 Chain J: N.56 Ligands: NAG.46 Ligand excluded by PLIP SO4.50: 5 residues within 4Å: Chain J: F.74, R.78 Chain L: E.30, K.71, R.96 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain J: R.158, E.163 Ligands: NAG.33 Ligand excluded by PLIP SO4.58: 3 residues within 4Å: Chain L: Q.224, D.225, R.226 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain M: P.7, T.8, E.9 Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain N: P.7, T.8, E.9 Ligand excluded by PLIP SO4.65: 3 residues within 4Å: Chain O: P.7, T.8, E.9 Ligand excluded by PLIP SO4.67: 3 residues within 4Å: Chain P: P.7, T.8, E.9 Ligand excluded by PLIP

16 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 CL.22: 1 residues within 4Å: Chain D: S.138 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain D: R.139 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain D: T.7, L.103 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain E: K.41, F.70, T.71 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Chain G: S.138 Ligand excluded by PLIP CL.38: 1 residues within 4Å: Chain G: R.139 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain G: T.7, L.103 Ligand excluded by PLIP CL.42: 3 residues within 4Å: Chain H: K.41, F.70, T.71 Ligand excluded by PLIP CL.52: 1 residues within 4Å: Chain J: S.138 Ligand excluded by PLIP CL.53: 1 residues within 4Å: Chain J: R.139 Ligand excluded by PLIP CL.54: 2 residues within 4Å: Chain J: T.7, L.103 Ligand excluded by PLIP CL.57: 3 residues within 4Å: Chain K: K.41, F.70, T.71 Ligand excluded by PLIP

8 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:R.245 NA.14: 2 residues within 4Å: Chain C: H.166, S.167 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.166, C:S.167 NA.25: 4 residues within 4Å: Chain D: Q.230, G.232, R.245, T.247 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.230 NA.29: 2 residues within 4Å: Chain F: H.166, S.167 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:H.166, F:S.167 NA.40: 4 residues within 4Å: Chain G: Q.230, G.232, R.245, T.247 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.230 NA.44: 2 residues within 4Å: Chain I: H.166, S.167 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:H.166, I:S.167 NA.55: 4 residues within 4Å: Chain J: Q.230, G.232, R.245, T.247 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:R.245 NA.59: 2 residues within 4Å: Chain L: H.166, S.167 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:H.166, L:S.167

4 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.15 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 6UL.26: 18 residues within 4Å: Chain D: 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.30 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:V.11, D:Q.13, D:A.46, D:F.69, D:F.69, D:Y.72, D:F.76, D:L.113, D:F.122, D:F.143, D:F.143, D:F.143 Hydrogen bonds: D:A.116 6UL.41: 18 residues within 4Å: Chain G: 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.45 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:V.11, G:Q.13, G:A.46, G:F.69, G:F.69, G:Y.72, G:F.76, G:L.113, G:F.122, G:F.143, G:F.143, G:F.143 Hydrogen bonds: G:A.116 6UL.56: 18 residues within 4Å: Chain J: 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.60 13 PLIP interactions: 13 interactions with chain J Hydrophobic interactions: J:V.11, J:Q.13, J:A.46, J:F.69, J:F.69, J:Y.72, J:F.76, J:L.113, J:F.122, J:F.143, J:F.143, J:F.143 Hydrogen bonds: J:A.116

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

70E.15: 32 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: Y.31, P.95, R.96, L.97, A.98, G.99, D.100 Ligands: 6UL.11 27 PLIP interactions: 21 interactions with chain A, 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, C:R.96, C:L.97 Hydrogen bonds: A:G.152, A:G.152, A:I.153, A:T.156, C:Y.31, C:A.98, C:G.99, C:D.100 70E.30: 32 residues within 4Å: Chain D: 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 F: Y.31, P.95, R.96, L.97, A.98, G.99, D.100 Ligands: 6UL.26 27 PLIP interactions: 6 interactions with chain F, 21 interactions with chain D Hydrophobic interactions: F:R.96, F:L.97, D:V.11, D:L.65, D:L.65, D:F.69, D:V.71, D:Y.72, D:Y.72, D:Y.72, D:F.76, D:L.113, D:L.123, D:V.125, D:I.147, D:I.147, D:V.157, D:L.161, D:Y.168 Hydrogen bonds: F:Y.31, F:A.98, F:G.99, F:D.100, D:G.152, D:G.152, D:I.153, D:T.156 70E.45: 32 residues within 4Å: Chain G: 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 I: Y.31, P.95, R.96, L.97, A.98, G.99, D.100 Ligands: 6UL.41 26 PLIP interactions: 5 interactions with chain I, 21 interactions with chain G Hydrophobic interactions: I:R.96, I:L.97, G:V.11, G:L.65, G:L.65, G:F.69, G:V.71, G:Y.72, G:Y.72, G:Y.72, G:F.76, G:L.113, G:L.123, G:V.125, G:I.147, G:I.147, G:V.157, G:L.161, G:Y.168 Hydrogen bonds: I:A.98, I:G.99, I:D.100, G:G.152, G:G.152, G:I.153, G:T.156 70E.60: 32 residues within 4Å: Chain J: 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 L: Y.31, P.95, R.96, L.97, A.98, G.99, D.100 Ligands: 6UL.56 26 PLIP interactions: 5 interactions with chain L, 21 interactions with chain J Hydrophobic interactions: L:R.96, L:L.97, J:V.11, J:L.65, J:L.65, J:F.69, J:V.71, J:Y.72, J:Y.72, J:Y.72, J:F.76, J:L.113, J:L.123, J:V.125, J:I.147, J:I.147, J:V.157, J:L.161, J:Y.168 Hydrogen bonds: L:A.98, L:G.99, L:D.100, J:G.152, J:G.152, J:I.153, J:T.156

4 x CS: CESIUM ION(Non-covalent)

CS.62: 2 residues within 4Å: Chain M: R.59, K.81 No protein-ligand interaction detected (PLIP) CS.64: 2 residues within 4Å: Chain N: R.59, K.81 No protein-ligand interaction detected (PLIP) CS.66: 2 residues within 4Å: Chain O: R.59, K.81 No protein-ligand interaction detected (PLIP) CS.68: 2 residues within 4Å: Chain P: R.59, K.81 No protein-ligand interaction detected (PLIP)

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: ADGJ
Beta-2-microglobulin: BEHK
GEM42 TCR beta chain: CFIL
GEM42 TCR alpha chain: MNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

B
B

E
B

H
B

K
B

C
E

F
E

I
E

L
E

M
D

N
D

O
D

P
D

T-cell surface glycoprotein CD1b

Beta-2-microglobulin

GEM42 TCR beta chain

GEM42 TCR alpha chain

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