SMTL ID : 1gzp.1

CD1b in complex with GM2 ganglioside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GM2: N-[(1S,2S)-2-HYDROXY-1-({[(2R,3R,4S,5S,6R)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-YL]OXY}METHYL)OCTADECYL]OCTADECANAMIDE(Non-covalent)

GM2.1: 23 residues within 4Å: Chain A: F.13, V.15, L.69, I.72, V.75, Y.76, G.79, F.80, A.103, V.129, S.133, C.134, G.156, I.157, M.158, T.160, V.161, L.164, L.165, C.169, Y.172 Ligands: D12.2, TWT.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.13, A:V.15, A:L.69, A:I.72, A:V.75, A:Y.76, A:Y.76, A:Y.76, A:F.80, A:A.103, A:V.129, A:V.161, A:L.165, A:Y.172 Hydrogen bonds: A:T.160

1 x D12: DODECANE(Non-covalent)

D12.2: 7 residues within 4Å: Chain A: E.83, F.87, F.91, M.93, F.147, Y.154 Ligands: GM2.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.83, A:E.83, A:F.87, A:F.87, A:F.91, A:F.91, A:F.147, A:Y.154

1 x TWT: DOCOSANE(Non-covalent)

TWT.3: 14 residues within 4Å: Chain A: V.15, I.16, Q.17, H.41, W.43, Y.76, F.80, I.99, G.101, A.103, G.119, F.126, Y.172 Ligands: GM2.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.15, A:V.15, A:Q.17, A:W.43, A:Y.76, A:F.80, A:I.99, A:A.103, A:F.126, A:Y.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gadola, S.D. et al., Structure of human CD1b with bound ligands at 2.3 A, a maze for alkyl chains. Nat. Immunol. (2002)

Release Date

2002-07-31

Peptides

T-CELL SURFACE GLYCOPROTEIN CD1B: A
B2-MICROGLOBULIN: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

T-CELL SURFACE GLYCOPROTEIN CD1B

B2-MICROGLOBULIN

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