SMTL ID : 6c6f.1

Structure of glycolipid aGSA[26,P5p] in complex with mouse CD1d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- 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-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.1: 9 residues within 4Å: Chain A: E.113, S.114, F.128, W.129, G.130, T.131, Q.161, L.164, N.165 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.128, A:L.164 Hydrogen bonds: A:S.114, A:S.114, A:G.130 Water bridges: A:T.131

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

NAG.2: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.22, A:S.22 NAG.3: 5 residues within 4Å: Chain A: W.23, S.24, R.25, N.42, D.43 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:R.25, A:N.42

1 x ELS: N-[(2S,3S,4R)-3,4-dihydroxy-8-oxo-8-[(4-pentylphenyl)amino]-1-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetr ahydro-2H-pyran-2-yl]oxy}octan-2-yl]hexacosanamide(Non-covalent)

ELS.4: 31 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, W.40, I.47, L.66, F.70, Y.73, S.76, F.77, R.79, D.80, I.98, L.100, L.116, V.118, F.120, V.126, W.133, W.142, L.143, L.150, D.153, G.155, T.156, T.159, V.160, C.168, F.171 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:F.10, A:V.30, A:W.40, A:I.47, A:L.66, A:F.70, A:Y.73, A:Y.73, A:I.98, A:L.100, A:L.116, A:V.118, A:F.120, A:V.126, A:W.142, A:L.143, A:L.150, A:T.159, A:V.160, A:F.171 Hydrogen bonds: A:S.76, A:R.79, A:G.155, A:T.156, A:T.156 Water bridges: A:Y.73, A:D.153 pi-Stacking: A:W.133

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

NA.5: 7 residues within 4Å: Chain A: E.97, I.98, Q.99, A.119, F.120, Q.121, G.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.99, A:Q.99, A:G.122 NA.6: 6 residues within 4Å: Chain A: F.115, L.116, H.117, R.127, F.128, W.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.116, A:F.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zajonc, D.M. et al., Structure-function analysis of sphingamides. To Be Published

Release Date

2019-01-30

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

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