SMTL ID : 5ajc.1

X-ray structure of RSL lectin in complex with sialyl lewis X tetrasaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-trimer

Ligands

1 x NDG- FUC- GAL: alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-functional Binders)

NDG-FUC-GAL.1: 10 residues within 4Å: Chain A: R.17, E.28, Y.37, G.39, A.40, F.41, I.59, I.61, W.76, W.81 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.59, A:I.61 Hydrogen bonds: A:R.17, A:E.28, A:A.40, A:F.41, A:R.17 Water bridges: A:Y.37, A:Y.37

1 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-FUC.2: 11 residues within 4Å: Chain B: R.17, E.28, D.32, Y.37, G.39, A.40, F.41, I.59, I.61, W.76, W.81 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.59, B:I.61 Hydrogen bonds: B:R.17, B:E.28, B:A.40, B:F.41, B:R.17 Water bridges: B:T.38, B:D.32, B:D.32

1 x NDG- GAL- SIA- FUC: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG-GAL-SIA-FUC.3: 12 residues within 4Å: Chain C: R.17, E.28, D.32, Y.37, G.39, A.40, F.41, I.61, W.76, N.79, G.80, W.81 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.61, C:W.76 Hydrogen bonds: C:R.17, C:E.28, C:Y.37, C:A.40, C:F.41, C:R.17, C:N.79, C:W.81 Water bridges: C:T.38, C:G.39

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 6 residues within 4Å: Chain A: S.2, V.3, N.22, N.23 Chain C: G.68, T.69 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:V.3, A:N.22, A:N.23, A:N.23, C:G.68 Water bridges: A:G.24

3 x FUL: beta-L-fucopyranose(Non-covalent)

FUL.5: 10 residues within 4Å: Chain A: W.53, R.62, E.73, G.84, A.85, Y.86 Chain B: P.14, I.16, W.31, W.36 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.53, B:I.16 Hydrogen bonds: A:E.73, A:A.85, A:Y.86 Salt bridges: A:R.62 FUL.7: 11 residues within 4Å: Chain B: W.53, R.62, E.73, G.84, A.85, Y.86 Chain C: P.14, I.16, W.31, W.36 Ligands: FUC.6 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.53, C:I.16 Hydrogen bonds: B:R.62, B:E.73, B:A.85, B:Y.86 Salt bridges: B:R.62 FUL.9: 10 residues within 4Å: Chain A: P.14, I.16, W.31, W.36 Chain C: R.62, E.73, G.84, A.85, Y.86 Ligands: FUC.8 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:I.16 Hydrogen bonds: C:R.62, C:E.73, C:A.85, C:Y.86 Salt bridges: C:R.62

2 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.6: 11 residues within 4Å: Chain B: W.53, R.62, E.73, G.84, A.85, Y.86 Chain C: P.14, I.16, W.31, W.36 Ligands: FUL.7 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.53, C:I.16 Hydrogen bonds: B:E.73, B:A.85, B:Y.86 Salt bridges: B:R.62 FUC.8: 10 residues within 4Å: Chain A: P.14, I.16, W.31, W.36 Chain C: R.62, E.73, G.84, A.85, Y.86 Ligands: FUL.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.62, C:E.73, C:A.85, C:Y.86 Salt bridges: C:R.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Topin, J. et al., The Hidden Conformation of Lewis X, a Human Histo-Blood Group Antigen, is a Determinant for Recognition by Pathogen Lectins. Acs Chem.Biol. (2016)

Release Date

2016-03-02

Peptides

PUTATIVE FUCOSE-BINDING LECTIN PROTEIN: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

PUTATIVE FUCOSE-BINDING LECTIN PROTEIN

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