SMTL ID : 5mxg.1

Photorhabdus asymbiotica lectin (PHL) in complex with blood group H trisaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

6 x NAG- GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-GAL-FUC.1: 8 residues within 4Å: Chain A: K.75, G.76, Q.77, G.98, T.99, W.104, N.117, W.118 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.104 Hydrogen bonds: A:Q.77, A:T.99, A:T.99, A:G.76, A:N.117, A:W.118, A:W.118 Water bridges: A:Q.77, A:W.118 NAG-GAL-FUC.2: 9 residues within 4Å: Chain A: N.170, G.171, V.172, G.193, T.194, W.199, S.213, W.214, E.215 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.199, A:E.215 Hydrogen bonds: A:V.172, A:T.194, A:T.194, A:G.171, A:W.214, A:W.214, A:W.214 NAG-GAL-FUC.3: 7 residues within 4Å: Chain A: N.314, G.315, V.316, G.337, T.338, W.343, W.355 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.343 Hydrogen bonds: A:V.316, A:T.338, A:T.338, A:G.315, A:W.355, A:W.355, A:W.355 NAG-GAL-FUC.5: 8 residues within 4Å: Chain B: K.75, G.76, Q.77, G.98, T.99, W.104, N.117, W.118 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.104 Hydrogen bonds: B:Q.77, B:T.99, B:T.99, B:G.76, B:N.117, B:W.118, B:W.118 Water bridges: B:Q.77, B:W.118 NAG-GAL-FUC.6: 9 residues within 4Å: Chain B: N.170, G.171, V.172, G.193, T.194, W.199, S.213, W.214, E.215 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.199, B:E.215 Hydrogen bonds: B:V.172, B:T.194, B:T.194, B:G.171, B:W.214, B:W.214, B:W.214 NAG-GAL-FUC.7: 7 residues within 4Å: Chain B: N.314, G.315, V.316, G.337, T.338, W.343, W.355 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.343 Hydrogen bonds: B:V.316, B:T.338, B:T.338, B:G.315, B:W.355, B:W.355, B:W.355

2 x NA: SODIUM ION(Non-covalent)

NA.4: 2 residues within 4Å: Chain A: T.178, V.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.178, A:V.179 NA.8: 2 residues within 4Å: Chain B: T.178, V.179 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.178, B:T.178, B:V.179

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Jancarikova, G. et al., Characterization of novel bangle lectin from Photorhabdus asymbiotica with dual sugar-binding specificity and its effect on host immunity. PLoS Pathog. (2017)

Release Date

2017-08-09

Peptides

Photorhabdus asymbiotica lectin PHL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Photorhabdus asymbiotica lectin PHL

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