SMTL ID : 6rgw.1

Photorhabdus asymbiotica lectin PHL in complex with O-methylated PGL-1-derived disaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

K3Q.1: 9 residues within 4Å: Chain A: G.76, Q.77, V.78, G.98, T.99, D.100, W.104, W.118 Ligands: 7CV.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.77, A:T.99, A:T.99, A:D.100, A:W.104 K3Q.3: 9 residues within 4Å: Chain A: G.171, V.172, I.173, G.193, T.194, D.195, W.199, W.214 Ligands: 7CV.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.172, A:T.194, A:D.195, A:W.199 K3Q.6: 8 residues within 4Å: Chain A: G.219, I.220, I.221, G.241, A.242, D.243, W.247, W.262 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.220, A:A.242, A:W.247 K3Q.8: 6 residues within 4Å: Chain A: G.315, V.316, I.317, T.338, W.343, W.355 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.316, A:V.316, A:T.338 K3Q.9: 8 residues within 4Å: Chain A: G.49, T.50, D.51, W.55, W.71, G.360, V.361, L.362 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.50, A:T.50, A:D.51, A:V.361 K3Q.13: 9 residues within 4Å: Chain B: G.76, Q.77, V.78, G.98, T.99, D.100, W.104, W.118 Ligands: 7CV.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.77, B:T.99, B:D.100, B:W.104 K3Q.15: 9 residues within 4Å: Chain B: G.171, V.172, I.173, G.193, T.194, D.195, W.199, W.214 Ligands: 7CV.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.172, B:T.194, B:D.195, B:W.199 K3Q.18: 8 residues within 4Å: Chain B: G.219, I.220, I.221, G.241, A.242, D.243, W.247, W.262 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.220, B:A.242, B:W.247 K3Q.20: 6 residues within 4Å: Chain B: G.315, V.316, I.317, T.338, W.343, W.355 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.316, B:V.316, B:T.338 K3Q.21: 8 residues within 4Å: Chain B: G.49, T.50, D.51, W.55, W.71, G.360, V.361, L.362 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.50, B:D.51, B:V.361

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

7CV.2: 5 residues within 4Å: Chain A: K.75, G.76, Q.77, W.118 Ligands: K3Q.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.118 Hydrogen bonds: A:G.76 7CV.4: 3 residues within 4Å: Chain A: W.214 Ligands: K3Q.3, K42.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.214 7CV.14: 5 residues within 4Å: Chain B: K.75, G.76, Q.77, W.118 Ligands: K3Q.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.118 Hydrogen bonds: B:G.76 7CV.16: 3 residues within 4Å: Chain B: W.214 Ligands: K3Q.15, K42.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.214

2 x K42: 4-(2-azanylethoxy)phenol(Non-covalent)

K42.5: 2 residues within 4Å: Chain A: S.213 Ligands: 7CV.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.213, A:S.213 K42.17: 2 residues within 4Å: Chain B: S.213 Ligands: 7CV.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.213, B:S.213

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

EDO.7: 5 residues within 4Å: Chain A: G.267, V.268, G.289, T.290, W.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.268, A:T.290, A:T.290 EDO.19: 5 residues within 4Å: Chain B: G.267, V.268, G.289, T.290, W.295 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.268, B:T.290, B:T.290

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

NA.10: 4 residues within 4Å: Chain A: E.284, H.296, Q.347, W.352 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.296, A:Q.347 Water bridges: A:N.278 NA.11: 2 residues within 4Å: Chain A: N.37, T.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.37 NA.22: 4 residues within 4Å: Chain B: E.284, H.296, Q.347, W.352 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.296, B:Q.347, B:W.352 Water bridges: B:N.278 NA.23: 2 residues within 4Å: Chain B: N.37, T.38 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:S.39, A:A.231

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

CL.12: 5 residues within 4Å: Chain A: T.26, I.27, A.28, T.222, R.240 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain B: T.26, I.27, A.28, T.222, R.240 Ligand excluded by PLIP

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 PHL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Lectin PHL

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