SMTL ID : 3t8x.1 (1 other biounit)

Crystal structure of human CD1b in complex with synthetic antigenic diacylsulfoglycolipid SGL12 and endogenous spacer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 3 residues within 4Å: Chain A: T.19, N.20, W.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.20

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

NAG-NAG-BMA-MAN-FUC.2: 6 residues within 4Å: Chain A: N.57, F.58, P.167, R.168, L.171, N.175 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.175, A:L.171 Water bridges: A:R.168

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

SO4.3: 2 residues within 4Å: Chain A: H.105, S.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.106 Salt bridges: A:H.105

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

ACT.4: 2 residues within 4Å: Chain A: R.262, K.264 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.262, A:K.264

1 x T8X: 2-O-sulfo-alpha-D-glucopyranosyl 2-O-hexadecanoyl-3-O-[(2E,4S,6S,8S)-2,4,6,8-tetramethyltetracos-2-enoyl]-alpha-D-glucopyranoside(Non-covalent)

T8X.5: 19 residues within 4Å: Chain A: F.10, I.69, V.72, Y.73, F.77, R.79, E.80, A.100, V.126, I.148, Y.151, Q.152, G.153, I.154, T.157, V.158, L.161, L.162 Ligands: ULI.6 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.10, A:I.69, A:V.72, A:F.77, A:A.100, A:V.126, A:I.148, A:I.148, A:Y.151, A:I.154, A:I.154, A:V.158, A:L.161, A:L.162 Hydrogen bonds: A:R.79, A:R.79, A:E.80 Water bridges: A:Q.152

1 x ULI: tetracontane(Non-covalent)

ULI.6: 25 residues within 4Å: Chain A: V.12, I.13, Q.14, S.29, H.38, W.40, F.70, Y.73, I.74, V.81, F.84, F.88, M.90, I.96, Q.97, G.98, I.99, L.114, G.116, F.123, F.144, L.147, Y.151, Y.169 Ligands: T8X.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.12, A:Q.14, A:H.38, A:W.40, A:I.74, A:F.84, A:F.88, A:F.88, A:F.88, A:I.96, A:I.96, A:L.114, A:F.123, A:F.123, A:F.123, A:L.147, A:Y.151, A:Y.169

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: G.233, D.234, R.246 Chain B: K.6, Q.8 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.6, B:K.6, A:D.234, A:R.246 Water bridges: A:L.232, A:R.246 GOL.8: 5 residues within 4Å: Chain B: K.41, E.69, F.70, T.71, Y.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.71, B:T.71, B:Y.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Alles, L.F. et al., Structural reorganization of the human CD1b Antigen-binding groove for presentation of mycobacterial sulfoglycolipids. To be Published

Release Date

2011-10-26

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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