SMTL ID : 6rgg.1

Photorhabdus laumondii lectin PLL2 in complex with O-methylated PGL-1-derived disaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

6 x K3Q: 3,6-O-dimethyl-D-glucose(Non-covalent)

K3Q.1: 6 residues within 4Å: Chain A: G.78, K.79, V.80, T.101, W.106, W.120 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.79, A:K.79, A:T.101, A:T.101 K3Q.2: 6 residues within 4Å: Chain A: G.269, V.270, G.291, T.292, Y.297, W.312 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.270, A:T.292, A:T.292 K3Q.3: 7 residues within 4Å: Chain A: G.317, T.318, G.339, T.340, W.345, W.357 Ligands: 7CV.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.318, A:T.340, A:T.340 K3Q.9: 8 residues within 4Å: Chain B: G.78, K.79, V.80, G.100, T.101, D.102, W.106, W.120 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.79, B:K.79, B:T.101, B:D.102 K3Q.10: 8 residues within 4Å: Chain B: G.125, T.126, I.127, G.147, T.148, W.153, W.168 Ligands: 7CV.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.126, B:T.148, B:T.148 K3Q.13: 7 residues within 4Å: Chain B: G.221, V.222, I.223, G.243, S.244, Y.249, W.264 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.222, B:V.222, B:S.244

2 x 7CV: 6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose(Non-covalent)

7CV.4: 3 residues within 4Å: Chain A: W.345, W.357 Ligands: K3Q.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.345 7CV.11: 2 residues within 4Å: Chain B: W.153 Ligands: K3Q.10 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.153

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

NA.5: 5 residues within 4Å: Chain A: N.89, T.90, V.135, G.139, H.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.90, A:T.90, A:H.161 NA.6: 5 residues within 4Å: Chain A: I.29, A.30, S.32, D.226, A.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.32, A:D.226 NA.7: 6 residues within 4Å: Chain A: N.136, T.137, G.187, Q.205, P.208, D.209 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.137, A:Q.205, A:D.209, A:D.209, A:D.209 NA.8: 8 residues within 4Å: Chain A: E.33, I.34, V.35, S.321, A.322, P.323, T.324, F.336 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.34, A:V.35, A:S.321, A:T.324 NA.14: 5 residues within 4Å: Chain B: N.136, T.137, G.187, Q.205, D.209 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.137, B:Q.205, B:D.209

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12: 3 residues within 4Å: Chain B: G.173, V.174, W.201 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.174

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Fujdiarova, E. et al., Heptabladed beta-propeller lectins PLL2 and PHL from Photorhabdus spp. recognize O-methylated sugars and influence the host immune system. Febs J. (2020)

Release Date

2020-07-01

Peptides

lectin PLL2 from Photorhabdus laumondii: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

lectin PLL2 from Photorhabdus laumondii

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