SMTL ID : 6f5w.1

Photorhabdus asymbiotica lectin (PHL) in complex with propargyl-fucoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 2 residues within 4Å: Chain A: T.178, V.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.178, A:V.179 NA.2: 2 residues within 4Å: Chain A: N.37, T.38 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.37, A:G.41 NA.3: 2 residues within 4Å: Chain A: D.229, T.230 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.229 NA.4: 3 residues within 4Å: Chain A: S.165, W.166, A.167 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.165 NA.20: 6 residues within 4Å: Chain A: S.39, D.40, T.111 Chain B: S.183, S.254, H.255 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.183, B:S.254, B:H.255, A:S.39 Water bridges: A:N.112 NA.21: 2 residues within 4Å: Chain B: T.178, V.179 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.178, B:V.179, B:V.179 NA.22: 2 residues within 4Å: Chain B: N.37, T.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.37 NA.23: 2 residues within 4Å: Chain B: D.229, T.230 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.229, B:D.229 NA.24: 1 residues within 4Å: Chain B: N.112 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.112 Water bridges: B:R.42

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

CL.5: 2 residues within 4Å: Chain A: P.306, W.307 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: N.117, W.118 Ligands: KG1.13 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: T.178, V.226, V.227 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: N.37, A.327 Chain B: N.281 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: G.70, W.71 Ligands: KG1.17 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: N.281 Chain B: N.37, A.327 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: S.165, W.166 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: P.162, W.163 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: R.336, I.363, D.364 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain B: T.178, V.226, V.227 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain B: K.52, T.79 Ligand excluded by PLIP

5 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.10: 6 residues within 4Å: Chain A: G.219, I.220, G.241, A.242, W.247, W.262 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.220, A:A.242 pi-Cation interactions: A:W.247, A:W.247, A:W.262 DMS.11: 6 residues within 4Å: Chain A: L.313, N.314, T.345, W.352, S.353, W.355 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.345 DMS.12: 6 residues within 4Å: Chain A: I.181, N.182, S.183, G.185 Chain B: T.88, G.90 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.90 DMS.30: 5 residues within 4Å: Chain B: G.219, I.220, G.241, A.242, W.247 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.220 pi-Cation interactions: B:W.247, B:W.247, B:W.262 DMS.31: 6 residues within 4Å: Chain A: T.88, G.90 Chain B: I.181, N.182, S.183, G.185 No protein-ligand interaction detected (PLIP)

11 x KG1: propadienyl 6-deoxy-alpha-L-galactopyranoside(Non-covalent)

KG1.13: 7 residues within 4Å: Chain A: G.76, Q.77, G.98, T.99, W.104, W.118 Ligands: CL.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.104, A:W.118 Hydrogen bonds: A:Q.77, A:Q.77, A:T.99 KG1.14: 6 residues within 4Å: Chain A: G.171, V.172, G.193, T.194, W.199, W.214 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.199, A:W.214 Hydrogen bonds: A:V.172, A:V.172, A:T.194 Water bridges: A:T.194, A:D.195 KG1.15: 6 residues within 4Å: Chain A: G.267, V.268, G.289, T.290, W.295, W.310 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.295 Hydrogen bonds: A:V.268, A:V.268, A:T.290 Water bridges: A:D.291, A:D.291 KG1.16: 6 residues within 4Å: Chain A: G.315, V.316, G.337, T.338, W.343, W.355 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.343 Hydrogen bonds: A:V.316, A:V.316, A:T.338 KG1.17: 7 residues within 4Å: Chain A: G.49, T.50, W.55, W.71, G.360, V.361 Ligands: CL.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.55 Hydrogen bonds: A:T.50, A:V.361, A:V.361 Water bridges: A:D.51 KG1.18: 11 residues within 4Å: Chain A: N.182, R.186, E.188, H.200, W.202, T.204, Q.251, H.255, S.256, G.257, W.259 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.202 Hydrogen bonds: A:N.182, A:R.186, A:R.186, A:E.188, A:H.200, A:Q.251, A:G.257 Water bridges: A:W.259 Salt bridges: A:R.186 KG1.32: 6 residues within 4Å: Chain B: G.76, Q.77, G.98, T.99, W.104, W.118 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.104, B:W.118, B:W.118 Hydrogen bonds: B:Q.77, B:Q.77, B:T.99 KG1.33: 6 residues within 4Å: Chain B: G.171, V.172, G.193, T.194, W.199, W.214 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.199, B:W.214 Hydrogen bonds: B:V.172, B:V.172, B:T.194 Water bridges: B:D.195 KG1.34: 6 residues within 4Å: Chain B: G.315, V.316, G.337, T.338, W.343, W.355 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.343 Hydrogen bonds: B:V.316, B:V.316, B:T.338 Water bridges: B:D.339 KG1.35: 6 residues within 4Å: Chain B: G.49, T.50, W.55, W.71, G.360, V.361 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.55 Hydrogen bonds: B:T.50, B:V.361, B:V.361 KG1.36: 11 residues within 4Å: Chain B: N.182, R.186, E.188, H.200, W.202, T.204, Q.251, H.255, S.256, G.257, W.259 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.182, B:R.186, B:R.186, B:E.188, B:H.200, B:Q.251, B:G.257, B:W.259 Salt bridges: B:R.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jancarikova, G. et al., Synthesis of alpha-l-Fucopyranoside-Presenting Glycoclusters and Investigation of Their Interaction with Photorhabdus asymbiotica Lectin (PHL). Chemistry (2018)

Release Date

2018-01-31

Peptides

lectin PHL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

lectin PHL

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