SMTL ID : 6fhx.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: N.134, T.135, G.185, Q.203, P.206, D.207 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.135, A:D.207, A:D.207, A:D.207 NA.14: 8 residues within 4Å: Chain B: E.31, I.32, V.33, S.319, A.320, P.321, T.322, F.334 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.32, B:V.33, B:S.319, B:S.319, B:T.322

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

CL.2: 3 residues within 4Å: Chain A: R.336, I.363, D.364 Ligand excluded by PLIP

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

DSQ.3: 6 residues within 4Å: Chain A: K.75, G.76, Q.77, G.98, T.99, W.104 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.104 Hydrogen bonds: A:K.75, A:K.75, A:G.76, A:Q.77, A:T.99, A:T.99 DSQ.4: 8 residues within 4Å: Chain A: N.170, G.171, V.172, I.173, G.193, T.194, W.199, W.214 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.173, A:W.199, A:W.214 Hydrogen bonds: A:G.171, A:V.172, A:T.194, A:T.194 DSQ.5: 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 DSQ.6: 5 residues within 4Å: Chain A: G.315, V.316, G.337, T.338, W.343 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.343 Hydrogen bonds: A:V.316, A:T.338, A:T.338 DSQ.7: 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 DSQ.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:K.75, B:G.76, B:Q.77, B:T.99, B:T.99 DSQ.9: 6 residues within 4Å: Chain B: G.171, V.172, I.173, G.193, T.194, W.199 6 PLIP interactions: 6 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 DSQ.10: 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 DSQ.11: 6 residues within 4Å: Chain B: G.267, V.268, G.289, T.290, W.295, W.310 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.295, B:W.310 Hydrogen bonds: B:V.268, B:T.290, B:T.290 DSQ.12: 6 residues within 4Å: Chain B: G.315, V.316, I.317, G.337, T.338, W.343 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.317, B:W.343 Hydrogen bonds: B:V.316, B:T.338, B:T.338 DSQ.13: 6 residues within 4Å: Chain B: G.49, T.50, W.55, G.360, V.361, L.362 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.55, B:L.362 Hydrogen bonds: B:T.50, B:T.50, B:V.361

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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