SMTL ID : 6rgu.1

Photorhabdus asymbiotica lectin PHL in complex with 3-O-methyl-D-glucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

3MG.1: 6 residues within 4Å: Chain A: G.76, Q.77, G.98, T.99, W.104, W.118 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.77, A:T.99, A:T.99 Water bridges: A:T.99 3MG.2: 9 residues within 4Å: Chain A: N.87, R.91, E.93, H.105, W.107, Q.155, H.159, G.161, W.163 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.87, A:R.91, A:R.91, A:Q.155, A:G.161, A:W.163 Water bridges: A:W.163 Salt bridges: A:H.105 3MG.3: 6 residues within 4Å: Chain A: G.171, V.172, G.193, T.194, W.199, W.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.172, A:V.172, A:T.194 3MG.4: 7 residues within 4Å: Chain A: G.219, I.220, G.241, A.242, D.243, W.247, W.262 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.220, A:I.220, A:A.242, A:D.243 Water bridges: A:D.243, A:D.243 3MG.5: 9 residues within 4Å: Chain A: N.182, R.186, E.188, H.200, W.202, E.215, Q.251, G.257, W.259 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.182, A:R.186, A:R.186, A:Q.251, A:W.259 Water bridges: A:G.257 Salt bridges: A:H.200 3MG.6: 6 residues within 4Å: Chain A: G.315, V.316, G.337, T.338, W.343, W.355 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.316, A:T.338, A:T.338, A:T.338 Water bridges: A:T.338 3MG.7: 8 residues within 4Å: Chain A: N.278, R.282, E.284, H.296, W.298, Q.347, S.351, W.352 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.278, A:R.282, A:R.282, A:Q.347, A:S.350, A:W.352 Salt bridges: A:H.296 3MG.8: 7 residues within 4Å: Chain A: G.49, T.50, W.55, W.71, G.360, V.361, L.362 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.50, A:T.50, A:V.361 Water bridges: A:T.50, A:T.50, A:G.360 3MG.17: 6 residues within 4Å: Chain B: G.76, Q.77, G.98, T.99, W.104, W.118 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.77, B:T.99, B:T.99, B:T.99 Water bridges: B:T.99 3MG.18: 9 residues within 4Å: Chain B: N.87, R.91, E.93, H.105, W.107, Q.155, H.159, G.161, W.163 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.87, B:R.91, B:R.91, B:Q.155, B:G.161, B:W.163 Water bridges: B:W.163 Salt bridges: B:H.105 3MG.19: 6 residues within 4Å: Chain B: G.171, V.172, G.193, T.194, W.199, W.214 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.172, B:V.172, B:T.194 3MG.20: 7 residues within 4Å: Chain B: G.219, I.220, G.241, A.242, D.243, W.247, W.262 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.220, B:I.220, B:A.242, B:D.243 Water bridges: B:D.243 3MG.21: 9 residues within 4Å: Chain B: N.182, R.186, E.188, H.200, W.202, E.215, Q.251, G.257, W.259 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.182, B:R.186, B:R.186, B:Q.251, B:W.259 Water bridges: B:E.215, B:G.257 Salt bridges: B:H.200 3MG.22: 6 residues within 4Å: Chain B: G.315, V.316, G.337, T.338, W.343, W.355 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.316, B:T.338, B:T.338, B:T.338 3MG.23: 8 residues within 4Å: Chain B: N.278, R.282, E.284, H.296, W.298, Q.347, S.351, W.352 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.278, B:R.282, B:R.282, B:Q.347, B:S.350, B:W.352 Salt bridges: B:H.296 3MG.24: 7 residues within 4Å: Chain B: G.49, T.50, W.55, W.71, G.360, V.361, L.362 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.50, B:T.50, B:V.361 Water bridges: B:T.50, B:G.360

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 3 residues within 4Å: Chain A: N.37, A.327 Chain B: N.281 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: S.165, W.166 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: T.230, L.283, Q.299, H.303 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: R.336, I.363, D.364 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: S.39 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain A: N.281 Chain B: N.37, A.327 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: S.165, W.166 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain B: T.230, L.283, Q.299, H.303 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain B: R.336, I.363, D.364 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain B: S.39 Ligand excluded by PLIP

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

NA.14: 2 residues within 4Å: Chain A: N.37, T.38 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.231 NA.15: 4 residues within 4Å: Chain A: H.180, I.228, D.229, K.277 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.229, A:K.277, A:K.277 NA.16: 5 residues within 4Å: Chain A: T.135, G.137 Chain B: T.135, G.137 Ligands: NA.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.135 NA.30: 2 residues within 4Å: Chain B: N.37, T.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.37 NA.31: 4 residues within 4Å: Chain B: H.180, I.228, D.229, K.277 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.180, B:D.229, B:K.277 NA.32: 5 residues within 4Å: Chain A: T.135, G.137 Chain B: T.135, G.137 Ligands: NA.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.135

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 PHL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Lectin PHL

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