SMTL ID : 5mxf.1

Photorhabdus asymbiotica lectin (PHL) in complex with alpha-methyl fucoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x MFU: methyl alpha-L-fucopyranoside(Non-covalent)

MFU.1: 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 MFU.2: 6 residues within 4Å: Chain A: G.171, V.172, G.193, T.194, W.199, W.214 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.199 Hydrogen bonds: A:V.172, A:T.194, A:T.194 MFU.15: 5 residues within 4Å: Chain B: G.315, V.316, G.337, T.338, W.343 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.343 Hydrogen bonds: B:V.316, B:T.338, B:T.338 MFU.16: 6 residues within 4Å: Chain B: G.171, V.172, G.193, T.194, W.199, W.214 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.199 Hydrogen bonds: B:V.172, B:T.194, B:T.194

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

NA.3: 2 residues within 4Å: Chain A: T.178, V.179 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.178, A:V.179, A:V.179 Water bridges: A:I.131 NA.4: 1 residues within 4Å: Chain A: K.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.81, A:K.81 Water bridges: A:E.31 NA.5: 2 residues within 4Å: Chain A: T.38, D.40 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.38, A:T.38 Water bridges: A:D.40, A:E.44 NA.6: 2 residues within 4Å: Chain A: N.37, T.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.37 NA.17: 2 residues within 4Å: Chain B: T.178, V.179 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.179, B:V.179 Water bridges: B:I.131 NA.18: 1 residues within 4Å: Chain B: K.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.81, B:K.81 NA.19: 2 residues within 4Å: Chain B: T.38, D.40 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.40 Water bridges: B:D.40 NA.20: 2 residues within 4Å: Chain B: N.37, T.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.38

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

CL.7: 3 residues within 4Å: Chain A: T.178, V.226, V.227 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: P.67 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain A: G.49, T.50, D.51, K.52, A.53, W.55 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: N.117, W.118 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: S.309, W.310 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: R.336, I.363, D.364 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: E.215, S.216 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: N.281 Chain B: N.37, A.327 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: T.178, V.226, V.227 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain B: P.67 Ligand excluded by PLIP CL.23: 6 residues within 4Å: Chain B: G.49, T.50, D.51, K.52, A.53, W.55 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain B: N.117, W.118 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: S.309, W.310 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: R.336, I.363, D.364 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain B: E.215, S.216 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain A: N.37, A.327 Chain B: N.281 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jancarikova, G. et al., Characterization of novel bangle lectin from Photorhabdus asymbiotica with dual sugar-binding specificity and its effect on host immunity. PLoS Pathog. (2017)

Release Date

2017-08-09

Peptides

Photorhabdus asymbiotica lectin PHL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Photorhabdus asymbiotica lectin PHL

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