SMTL ID : 6fhy.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

12 x DS8: (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{S},4~{R},6~{R})-2-(hydroxymethyl)-6-oxidanyl-oxan-4-yl]methyl]-6-methyl-oxane-3,4,5-triol(Non-covalent)

DS8.1: 6 residues within 4Å: Chain A: K.75, G.76, Q.77, G.98, T.99, W.104 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.104 Hydrogen bonds: A:Q.77, A:T.99, A:T.99 DS8.2: 7 residues within 4Å: Chain A: N.170, G.171, V.172, G.193, T.194, W.199, S.213 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.199 Hydrogen bonds: A:G.171, A:V.172, A:T.194, A:T.194, A:D.195 Water bridges: A:W.214 DS8.3: 7 residues within 4Å: Chain A: G.219, I.220, G.241, A.242, D.243, W.247, W.262 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.247, A:W.262 Hydrogen bonds: A:I.220, A:A.242, A:D.243 DS8.4: 6 residues within 4Å: Chain A: G.267, V.268, I.269, G.289, T.290, W.295 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.269, A:W.295 Hydrogen bonds: A:V.268, A:T.290, A:T.290 Water bridges: A:D.291 DS8.5: 8 residues within 4Å: Chain A: N.314, G.315, V.316, G.337, T.338, W.343, P.354, W.355 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.343 Hydrogen bonds: A:G.315, A:V.316, A:T.338, A:T.338 Water bridges: A:W.355 DS8.6: 6 residues within 4Å: Chain A: G.49, T.50, W.55, G.360, V.361, L.362 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.55, A:L.362 Hydrogen bonds: A:T.50, A:T.50, A:G.360, A:V.361 Water bridges: A:D.51 DS8.8: 6 residues within 4Å: Chain B: K.75, G.76, Q.77, G.98, T.99, W.104 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.104 Hydrogen bonds: B:Q.77, B:T.99, B:T.99 Water bridges: B:G.76, B:W.118 DS8.9: 8 residues within 4Å: Chain B: N.170, G.171, V.172, I.173, G.193, T.194, D.195, W.199 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.173, B:W.199 Hydrogen bonds: B:G.171, B:V.172, B:T.194, B:T.194, B:D.195 DS8.10: 7 residues within 4Å: Chain B: G.219, I.220, G.241, A.242, D.243, W.247, W.262 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.247, B:W.262 Hydrogen bonds: B:I.220, B:A.242, B:D.243 Water bridges: B:G.219 DS8.11: 7 residues within 4Å: Chain B: G.267, V.268, I.269, G.289, T.290, W.295, W.310 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.269, B:W.295, B:W.310 Hydrogen bonds: B:V.268, B:T.290, B:T.290 DS8.12: 8 residues within 4Å: Chain B: N.314, G.315, V.316, G.337, T.338, W.343, P.354, W.355 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.343 Hydrogen bonds: B:V.316, B:T.338, B:T.338 Water bridges: B:W.355 DS8.13: 8 residues within 4Å: Chain B: G.49, T.50, D.51, W.55, W.71, G.360, V.361, L.362 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.55, B:L.362 Hydrogen bonds: B:T.50, B:T.50, B:D.51, B:G.360, B:V.361

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

CL.7: 3 residues within 4Å: Chain A: C.279, D.280, R.282 Ligand excluded by PLIP

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

EDO.14: 7 residues within 4Å: Chain B: N.182, R.186, E.188, H.200, W.202, Q.251, W.259 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.182, B:N.182, B:R.186, B:R.186, B:H.200, B:Q.251, B:W.259

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.15: 4 residues within 4Å: Chain B: T.50, D.339, N.340, V.361 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.339, B:N.340

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

2019-01-30

Peptides

Lectin PHL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lectin PHL

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