SMTL ID : 6flu.1

Photorhabdus asymbiotica lectin (PHL) in complex with synthetic C-fucoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

12 x DTK: (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{R},3~{S},4~{R},6~{S})-2-(hydroxymethyl)-6-methoxy-3-oxidanyl-oxan-4-yl]methyl]-6-methyl-oxane-3,4,5-triol(Non-covalent)

DTK.1: 7 residues within 4Å: Chain A: K.75, G.76, Q.77, G.98, T.99, W.104, W.118 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.104, A:W.118 Hydrogen bonds: A:G.76, A:Q.77, A:T.99, A:T.99 DTK.2: 6 residues within 4Å: Chain A: N.170, G.171, V.172, G.193, T.194, W.199 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.199 Hydrogen bonds: A:G.171, A:V.172, A:T.194, A:T.194 Water bridges: A:G.171 DTK.3: 8 residues within 4Å: Chain A: N.218, G.219, I.220, G.241, A.242, D.243, W.247, W.262 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.247, A:W.262 Hydrogen bonds: A:G.219, A:I.220, A:A.242, A:D.243 DTK.4: 5 residues within 4Å: Chain A: G.267, V.268, G.289, T.290, W.295 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.295 Hydrogen bonds: A:V.268, A:T.290, A:T.290 Water bridges: A:G.267, A:T.290 DTK.5: 6 residues within 4Å: Chain A: G.315, V.316, I.317, G.337, T.338, W.343 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.317, A:W.343 Hydrogen bonds: A:V.316, A:T.338, A:T.338 DTK.6: 6 residues within 4Å: Chain A: G.49, T.50, W.55, G.360, V.361, L.362 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.55, A:L.362 Hydrogen bonds: A:T.50, A:T.50, A:V.361 DTK.12: 6 residues within 4Å: Chain B: K.75, G.76, Q.77, G.98, T.99, W.104 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.104 Hydrogen bonds: B:G.76, B:Q.77, B:T.99, B:T.99 Water bridges: B:L.74, B:T.99 DTK.13: 6 residues within 4Å: Chain B: N.170, G.171, V.172, G.193, T.194, W.199 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.199 Hydrogen bonds: B:G.171, B:V.172, B:T.194, B:T.194 Water bridges: B:L.169, B:N.170 DTK.14: 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 Hydrophobic interactions: B:W.247, B:W.262 Hydrogen bonds: B:I.220, B:A.242, B:D.243 DTK.15: 5 residues within 4Å: Chain B: G.267, V.268, G.289, T.290, W.295 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.295 Hydrogen bonds: B:V.268, B:T.290, B:T.290 DTK.16: 7 residues within 4Å: Chain B: N.314, G.315, V.316, I.317, G.337, T.338, W.343 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.317, B:W.343 Hydrogen bonds: B:G.315, B:V.316, B:T.338, B:T.338 DTK.17: 6 residues within 4Å: Chain B: G.49, T.50, W.55, G.360, V.361, L.362 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.55, B:L.362 Hydrogen bonds: B:T.50, B:T.50, B:G.360, B:V.361

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

NA.7: 2 residues within 4Å: Chain A: S.25, K.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.369, A:K.369 NA.18: 2 residues within 4Å: Chain B: N.37, T.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.38 NA.19: 1 residues within 4Å: Chain B: S.168 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.168, B:S.168

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

CL.8: 2 residues within 4Å: Chain A: Q.311, S.312 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: R.336, I.363, D.364 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: P.306, W.307 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: T.26, I.27, A.28, T.222, R.240 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: T.26, I.27, A.28, T.222, R.240 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: Y.85, I.86 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Paulikova, G. et al., Fucosylated inhibitors of recently identified bangle lectin from Photorhabdus asymbiotica. Sci Rep (2019)

Release Date

2019-02-06

Peptides

Photorhabdus asymbitoca lectin PHL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Photorhabdus asymbitoca lectin PHL

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