SMTL ID : 4up4.1 (1 other biounit)

Structure of the recombinant lectin PVL from Psathyrella velutina in complex with GlcNAcb-D-1,3Galactoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

5 x GAL- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose(Non-covalent)

GAL-NAG.1: 9 residues within 4Å: Chain A: N.46, G.52, G.53, W.54, H.59, G.78, E.79, N.80, W.83 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.80, A:N.46, A:N.46, A:G.52, A:W.54, A:E.79 Water bridges: A:E.79, A:E.79, A:N.80, A:N.80 Hydrophobic interactions: A:W.54 GAL-NAG.2: 9 residues within 4Å: Chain A: N.159, Q.164, G.165, W.166, H.171, G.190, E.191, N.192, Y.195 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.192, A:N.159, A:N.159, A:Q.164, A:W.166, A:E.191 Water bridges: A:E.191, A:Y.195, A:Y.195, A:Q.193 Hydrophobic interactions: A:W.166 GAL-NAG.3: 8 residues within 4Å: Chain A: N.214, G.220, G.221, W.222, H.227, G.246, V.247, Y.251 8 PLIP interactions: 8 interactions with chain A Water bridges: A:V.247, A:Y.251, A:A.248, A:Y.251 Hydrophobic interactions: A:W.222 Hydrogen bonds: A:N.214, A:N.214, A:G.220, A:W.222, A:V.247 GAL-NAG.4: 8 residues within 4Å: Chain A: N.325, Q.330, G.331, W.332, H.337, G.356, E.357, N.358 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.358, A:N.325, A:N.325, A:Q.330, A:W.332, A:E.357 Water bridges: A:E.357, A:E.357, A:N.358 Hydrophobic interactions: A:W.332 GAL-NAG.5: 8 residues within 4Å: Chain A: D.270, S.275, G.276, W.277, H.282, G.301, D.302, Y.306 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.302, A:D.302, A:D.302, A:D.270, A:S.275, A:W.277, A:D.302, A:D.302, A:Y.306 Water bridges: A:D.302, A:Y.306, A:N.329, A:A.303 Hydrophobic interactions: A:W.277

3 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.343, T.345, D.347, C.349, D.351 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.343, A:T.345, A:D.347, A:C.349, H2O.16 CA.7: 5 residues within 4Å: Chain A: D.233, T.235, D.237, K.239, D.241 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.233, A:T.235, A:D.237, A:K.239, A:D.241, H2O.13 CA.8: 5 residues within 4Å: Chain A: D.177, T.179, D.181, L.183, D.185 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.177, A:T.179, A:D.181, A:L.183, A:D.185

1 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.9: 8 residues within 4Å: Chain A: N.103, G.109, W.111, H.116, G.135, D.136, Y.140 Ligands: NAG.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.111 Hydrogen bonds: A:N.103, A:N.103, A:G.109, A:G.109, A:W.111, A:D.136 Water bridges: A:G.137, A:Y.140

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.10: 8 residues within 4Å: Chain A: N.103, G.109, W.111, H.116, G.135, D.136, Y.140 Ligands: NDG.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.111 Hydrogen bonds: A:N.103, A:N.103, A:G.109, A:W.111, A:D.136 Water bridges: A:G.137, A:Y.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Audfray, A. et al., A Recombinant Fungal Lectin for Labeling Truncated Glycans on Human Cancer Cells. Plos One (2015)

Release Date

2015-01-28

Peptides

LECTIN PVL: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LECTIN PVL

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