SMTL ID : 2h26.1

human CD1b in complex with endogenous phosphatidylcholine and spacer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

2 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.23, A:N.20 Water bridges: A:N.20, A:T.22, A:T.22 NAG-FUC.2: 5 residues within 4Å: Chain A: N.57, F.58, R.168, L.171, G.172 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.175 Hydrogen bonds: A:R.168

1 x 6PL: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

6PL.3: 23 residues within 4Å: Chain A: F.10, V.12, L.66, I.69, F.70, V.72, Y.73, G.76, F.77, A.100, V.126, A.129, C.131, G.153, I.154, M.155, T.157, V.158, L.161, T.165, C.166, Y.169 Ligands: 6UL.4 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.10, A:V.12, A:L.66, A:I.69, A:F.70, A:Y.73, A:Y.73, A:Y.73, A:F.77, A:A.100, A:V.126, A:I.154, A:I.154, A:T.157, A:L.161, A:T.165, A:Y.169 Hydrogen bonds: A:T.157 Water bridges: A:Y.151, A:G.153

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

6UL.4: 27 residues within 4Å: Chain A: V.12, I.13, Q.14, S.29, H.38, W.40, F.70, Y.73, I.74, F.77, E.80, F.84, F.88, M.90, I.96, G.98, I.99, A.100, L.114, R.115, G.116, F.123, L.124, F.144, L.147, Y.151 Ligands: 6PL.3 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:V.12, A:V.12, A:Q.14, A:H.38, A:W.40, A:F.70, A:Y.73, A:I.74, A:F.77, A:E.80, A:E.80, A:F.84, A:F.88, A:F.88, A:I.96, A:I.96, A:F.123, A:F.123, A:F.123, A:L.124, A:F.144, A:F.144, A:L.147, A:Y.151

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: G.233, D.234, L.236, Y.244, L.245, R.246 Chain B: Q.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.234, A:R.246

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

SO4.6: 5 residues within 4Å: Chain A: G.119 Chain B: I.1, Q.2, H.31, P.32 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.1, B:Q.2 Salt bridges: B:H.31 Water bridges: A:G.119, A:G.119 SO4.7: 4 residues within 4Å: Chain B: K.41, F.70, T.71, Y.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.71, B:Y.78 Salt bridges: B:K.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Alles, L.F. et al., Endogenous phosphatidylcholine and a long spacer ligand stabilize the lipid-binding groove of CD1b. Embo J. (2006)

Release Date

2006-07-04

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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