SMTL ID : 5l2j.1

Crystal Structure of human CD1b in complex with C36-GMM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG-NAG-BMA-MAN-MAN-FUC-FUC.1: 6 residues within 4Å: Chain A: N.56, F.57, E.61, R.167, L.170, N.174 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.174, A:L.170 Water bridges: A:R.167

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

6UL.2: 23 residues within 4Å: Chain A: V.11, I.12, Q.13, S.28, H.37, W.39, A.46, F.69, Y.72, F.76, V.80, F.83, M.89, I.95, G.97, I.98, A.99, G.115, A.116, F.122, L.123, F.143 Ligands: 70E.8 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:V.11, A:V.11, A:V.11, A:Q.13, A:H.37, A:W.39, A:A.46, A:F.69, A:F.69, A:F.76, A:V.80, A:F.83, A:I.95, A:I.95, A:A.99, A:F.122, A:F.122, A:F.122, A:F.143, A:F.143, A:F.143, A:F.143

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

NAG.3: 5 residues within 4Å: Chain A: N.19, S.20, T.21, W.22 Ligands: ACT.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.21 Hydrogen bonds: A:T.21, A:T.21

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

ACT.4: 2 residues within 4Å: Chain A: L.117 Chain B: I.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.139 ACT.5: 1 residues within 4Å: Ligands: NAG.3 No protein-ligand interaction detected (PLIP)

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

CL.6: 3 residues within 4Å: Chain A: A.256, G.257, R.277 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: G.5, P.212, K.213 Ligand excluded by PLIP

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

70E.8: 24 residues within 4Å: Chain A: F.9, H.37, L.65, F.69, V.71, Y.72, G.75, F.76, E.79, A.99, L.113, V.125, C.130, I.147, Q.151, I.153, M.154, T.156, V.157, L.160, L.161, C.165, Y.168 Ligands: 6UL.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.9, A:F.69, A:V.71, A:Y.72, A:F.76, A:E.79, A:A.99, A:L.113, A:V.125, A:I.147, A:T.156, A:L.160, A:L.160, A:L.161, A:Y.168, A:Y.168 Hydrogen bonds: A:Q.151, A:Q.151

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

NA.9: 2 residues within 4Å: Chain B: L.87, S.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.88, B:S.88 Water bridges: B:Q.89

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

T-cell surface glycoprotein CD1b

Beta-2-microglobulin

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