SMTL ID : 6rg2.1

Photorhabdus laumondii lectin PLL2 in complex with 3-O-methyl-D-glucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

homo-dimer

Ligands

5 x ZB1: 3-O-methyl-alpha-D-glucopyranose(Non-covalent)

ZB1.1: 7 residues within 4Å: Chain A: G.78, K.79, G.100, T.101, W.106, W.120 Ligands: 3MG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.79, A:T.101 Water bridges: A:G.78 ZB1.3: 6 residues within 4Å: Chain A: G.125, T.126, G.147, T.148, W.153, W.168 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.126, A:T.126, A:T.148, A:T.148, A:T.148 ZB1.6: 7 residues within 4Å: Chain A: G.173, V.174, G.195, T.196, W.201, W.216 Ligands: 3MG.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.174, A:T.196, A:T.196, A:T.196 Water bridges: A:G.173 ZB1.17: 7 residues within 4Å: Chain B: G.173, V.174, G.195, T.196, W.201, W.216 Ligands: 3MG.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.174, B:T.196 Water bridges: B:G.173, B:T.196 ZB1.21: 7 residues within 4Å: Chain B: G.317, T.318, G.339, T.340, W.345, W.357 Ligands: 3MG.22 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.318, B:T.340, B:T.340, B:T.340 Water bridges: B:G.317

14 x 3MG: 3-O-methyl-beta-D-glucopyranose(Non-covalent)

3MG.2: 9 residues within 4Å: Chain A: G.78, K.79, V.80, G.100, T.101, D.102, W.106, W.120 Ligands: ZB1.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.79, A:K.79, A:T.101, A:D.102, A:D.102 Water bridges: A:T.101 3MG.4: 9 residues within 4Å: Chain A: R.93, E.95, H.107, W.109, Q.121, Q.157, H.161, G.163, W.165 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.93, A:R.93, A:Q.121, A:Q.157, A:H.161, A:W.165 Water bridges: A:G.163 Salt bridges: A:H.107 3MG.5: 7 residues within 4Å: Chain A: G.173, V.174, G.195, T.196, D.197, W.201 Ligands: ZB1.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.174, A:V.174, A:T.196, A:D.197 Water bridges: A:G.173, A:T.196, A:T.196 3MG.7: 7 residues within 4Å: Chain A: G.221, V.222, G.243, S.244, N.245, Y.249, W.264 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.222, A:S.244, A:S.244, A:N.245 Water bridges: A:N.245, A:Y.249, A:Y.249 3MG.8: 9 residues within 4Å: Chain A: N.184, R.188, E.190, H.202, W.204, D.217, Q.253, H.257, W.261 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.184, A:R.188, A:R.188, A:Q.253, A:W.261 Water bridges: A:D.217, A:D.217, A:G.259, A:G.259 Salt bridges: A:H.202 3MG.11: 8 residues within 4Å: Chain A: N.280, R.284, E.286, H.298, W.300, Q.349, P.352, W.354 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.280, A:R.284, A:R.284, A:Q.349, A:P.352, A:W.354 Water bridges: A:W.354 Salt bridges: A:H.298 3MG.12: 7 residues within 4Å: Chain A: G.51, T.52, W.57, W.73, G.362, S.363, L.364 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.52, A:T.52, A:S.363 Water bridges: A:T.52, A:G.362 3MG.13: 7 residues within 4Å: Chain B: G.78, K.79, G.100, T.101, D.102, W.106, W.120 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.79, B:T.101, B:T.101 Water bridges: B:D.102 3MG.15: 10 residues within 4Å: Chain B: N.89, R.93, E.95, H.107, W.109, Q.121, Q.157, H.161, G.163, W.165 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.89, B:R.93, B:R.93, B:Q.157, B:W.165 Water bridges: B:G.163, B:G.163 Salt bridges: B:H.107 3MG.16: 8 residues within 4Å: Chain B: G.173, V.174, G.195, T.196, D.197, W.201, W.216 Ligands: ZB1.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.174, B:V.174, B:T.196, B:D.197 3MG.19: 9 residues within 4Å: Chain B: N.184, R.188, E.190, H.202, W.204, D.217, Q.253, H.257, W.261 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.184, B:R.188, B:R.188, B:Q.253, B:W.261 Water bridges: B:D.217, B:D.217, B:G.259, B:G.259 Salt bridges: B:H.202 3MG.22: 7 residues within 4Å: Chain B: G.317, T.318, G.339, T.340, W.345, W.357 Ligands: ZB1.21 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.318, B:T.318, B:T.340 Water bridges: B:T.340, B:T.340, B:D.341, B:D.341 3MG.23: 7 residues within 4Å: Chain B: N.280, R.284, E.286, H.298, W.300, Q.349, W.354 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.280, B:R.284, B:R.284, B:Q.349, B:W.354 Salt bridges: B:H.298 3MG.24: 7 residues within 4Å: Chain B: G.51, T.52, W.57, W.73, G.362, S.363, L.364 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.52, B:T.52, B:S.363 Water bridges: B:T.52, B:G.362

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 5 residues within 4Å: Chain A: G.269, V.270, I.271, Y.297, W.312 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.271, A:Y.297, A:W.312 Hydrogen bonds: A:V.270, A:V.270 ACT.10: 5 residues within 4Å: Chain A: G.317, T.318, I.319, W.345, W.357 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.319, A:W.345, A:W.357 Hydrogen bonds: A:T.318, A:T.318 ACT.14: 5 residues within 4Å: Chain B: G.125, T.126, I.127, W.153, W.168 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.127, B:W.153, B:W.168 Hydrogen bonds: B:T.126 ACT.18: 5 residues within 4Å: Chain B: G.221, V.222, I.223, Y.249, W.264 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.223, B:Y.249, B:W.264 Hydrogen bonds: B:V.222 ACT.20: 5 residues within 4Å: Chain B: G.269, V.270, I.271, Y.297, W.312 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.271, B:Y.297, B:W.312 Hydrogen bonds: B:V.270

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

NA.25: 2 residues within 4Å: Chain B: D.186, R.188 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.188 Water bridges: B:R.188 NA.26: 4 residues within 4Å: Chain B: N.245, A.247, G.269, V.270 No protein-ligand interaction detected (PLIP)

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
B

B
A

lectin PLL2 from Photorhabdus laumondii

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