SMTL ID : 6rfz.1

Photorhabdus laumondii lectin PLL2 in complex with D-glucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 6 residues within 4Å: Chain A: E.46, H.58, R.60, Q.110, A.115, W.117 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.60 Hydrogen bonds: A:E.46, A:Q.110 Water bridges: A:R.60 Salt bridges: A:H.58, A:R.60 ACT.2: 5 residues within 4Å: Chain A: G.125, T.126, I.127, W.153, W.168 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.127, A:W.153, A:W.168 Hydrogen bonds: A:T.126, A:T.126 Water bridges: A:T.126 ACT.4: 5 residues within 4Å: Chain A: G.173, V.174, I.175, W.201, W.216 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.175, A:W.201, A:W.216 Hydrogen bonds: A:V.174, A:V.174 ACT.5: 4 residues within 4Å: Chain A: G.221, V.222, Y.249, W.264 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.249, A:W.264 Hydrogen bonds: A:V.222, A:V.222 ACT.7: 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.11: 5 residues within 4Å: Chain A: W.57, W.73, G.362, S.363, L.364 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.57, A:W.73, A:L.364 Hydrogen bonds: A:S.363, A:S.363 ACT.13: 6 residues within 4Å: Chain B: E.46, H.58, R.60, Q.110, A.115, W.117 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.60 Hydrogen bonds: B:E.46, B:Q.110 Water bridges: B:R.60 Salt bridges: B:H.58, B:R.60 ACT.14: 5 residues within 4Å: Chain B: G.125, T.126, I.127, W.153, W.168 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.127, B:W.153, B:W.168 Hydrogen bonds: B:T.126, B:T.126 ACT.16: 5 residues within 4Å: Chain B: G.173, V.174, I.175, W.201, W.216 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.175, B:W.201, B:W.216 Hydrogen bonds: B:V.174, B:V.174 ACT.17: 4 residues within 4Å: Chain B: G.221, V.222, Y.249, W.264 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.249, B:W.264 Hydrogen bonds: B:V.222, B:V.222 ACT.19: 5 residues within 4Å: Chain B: G.269, V.270, I.271, Y.297, W.312 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.271, B:Y.297, B:W.312 Hydrogen bonds: B:V.270, B:V.270 ACT.23: 5 residues within 4Å: Chain B: W.57, W.73, G.362, S.363, L.364 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.57, B:W.73, B:L.364 Hydrogen bonds: B:S.363, B:S.363

8 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.3: 10 residues within 4Å: Chain A: N.89, R.93, E.95, H.107, W.109, Q.121, Q.157, H.161, G.163, W.165 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.89, A:R.93, A:R.93, A:E.95, A:H.107, A:Q.157, A:G.163, A:W.165 Water bridges: A:R.93, A:Q.121, A:Q.121 BGC.6: 9 residues within 4Å: Chain A: N.184, R.188, E.190, H.202, W.204, Q.253, H.257, G.259, W.261 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.184, A:N.184, A:R.188, A:R.188, A:H.202, A:Q.253, A:G.259, A:W.261 Water bridges: A:R.188 BGC.8: 9 residues within 4Å: Chain A: T.232, R.236, E.238, H.250, W.252, L.285, Q.301, S.306, W.309 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.250, A:Q.301, A:W.309 Water bridges: A:R.236 Salt bridges: A:R.236 BGC.10: 7 residues within 4Å: Chain A: N.280, R.284, E.286, H.298, W.300, Q.349, W.354 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.280, A:N.280, A:R.284, A:R.284, A:H.298, A:Q.349, A:W.354 Water bridges: A:R.284 BGC.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 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.89, B:R.93, B:R.93, B:E.95, B:H.107, B:Q.157, B:G.163, B:W.165, B:W.165 Water bridges: B:R.93, B:Q.121, B:Q.121 BGC.18: 9 residues within 4Å: Chain B: N.184, R.188, E.190, H.202, W.204, Q.253, H.257, G.259, W.261 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.184, B:N.184, B:R.188, B:R.188, B:H.202, B:Q.253, B:G.259, B:W.261, B:W.261 Water bridges: B:R.188 BGC.20: 9 residues within 4Å: Chain B: T.232, R.236, E.238, H.250, W.252, L.285, Q.301, S.306, W.309 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.250, B:Q.301, B:W.309, B:W.309 Water bridges: B:R.236 Salt bridges: B:R.236 BGC.22: 7 residues within 4Å: Chain B: N.280, R.284, E.286, H.298, W.300, Q.349, W.354 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.280, B:N.280, B:R.284, B:R.284, B:H.298, B:Q.349, B:W.354, B:W.354 Water bridges: B:R.284

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

EDO.9: 4 residues within 4Å: Chain A: G.317, T.318, W.345, W.357 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.318 EDO.21: 4 residues within 4Å: Chain B: G.317, T.318, W.345, W.357 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.318

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

NA.12: 2 residues within 4Å: Chain A: S.36, V.85 6 PLIP interactions: 6 interactions with chain A Water bridges: A:V.35, A:V.37, A:V.37, A:K.83, A:K.83, A:K.83 NA.24: 2 residues within 4Å: Chain B: S.36, V.85 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.36 Water bridges: B:V.37, B:K.83, B:K.83

Links

RCSB   PDBe   PDBe-KB   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. (2021)

Release Date

2020-07-01

Peptides

lectin PLL2 from Photorhabdus laumondii: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

lectin PLL2 from Photorhabdus laumondii

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