SMTL ID : 5mb4.1

Crystal Structure of the Psathyrella asperospora lectin PAL in complex with GlcNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: D.177, I.178, T.179, N.181, L.183, D.185 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.178, A:T.179, A:N.181, A:L.183, A:D.185 Water bridges: A:N.199 NA.2: 7 residues within 4Å: Chain A: K.58, H.59, F.77, G.78, S.105, Y.106, R.118 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.77, A:Y.106, A:R.118, A:R.118 NA.3: 6 residues within 4Å: Chain A: D.233, L.234, T.235, D.237, R.239, D.241 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.233, A:L.234, A:T.235, A:R.239 NA.4: 5 residues within 4Å: Chain A: D.343, T.345, D.347, A.349, D.351 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.345, A:T.345, A:A.349 NA.5: 5 residues within 4Å: Chain A: D.65, T.67, D.69, Q.71, D.73 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.66, A:T.67, A:D.69, A:Q.71 NA.6: 3 residues within 4Å: Chain A: D.69, Q.71, N.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.87 Water bridges: A:N.87

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.7: 6 residues within 4Å: Chain A: D.169, R.170, V.217, T.223, I.224, A.225 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.224, A:A.225 Water bridges: A:R.170, A:R.170, A:R.170 Salt bridges: A:R.170

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

NAG.8: 9 residues within 4Å: Chain A: D.159, Q.164, G.165, W.166, H.171, G.190, E.191, F.195 Ligands: NDG.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.166 Hydrogen bonds: A:D.159, A:Q.164, A:W.166, A:E.191 Water bridges: A:N.192 NAG.10: 8 residues within 4Å: Chain A: N.46, G.52, G.53, W.54, H.59, G.78, E.79, W.83 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.54 Hydrogen bonds: A:N.46, A:N.46, A:G.52, A:W.54, A:E.79 Water bridges: A:D.80, A:D.80, A:G.81 NAG.11: 8 residues within 4Å: Chain A: D.270, S.275, G.276, W.277, H.282, G.301, D.302, Y.306 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.270, A:S.275, A:W.277, A:D.302, A:Y.306 Water bridges: A:A.303 NAG.12: 8 residues within 4Å: Chain A: N.214, G.220, G.221, W.222, H.227, G.246, G.247, Y.251 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.222 Hydrogen bonds: A:N.214, A:N.214, A:G.220, A:W.222, A:G.247, A:Y.251 Water bridges: A:A.248, A:A.248 NAG.13: 8 residues within 4Å: Chain A: N.325, Q.330, G.331, W.332, H.337, G.356, E.357, W.361 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.332 Hydrogen bonds: A:N.325, A:N.325, A:Q.330, A:W.332, A:E.357, A:N.358 Water bridges: A:Q.330, A:N.358, A:N.358 NAG.14: 10 residues within 4Å: Chain A: N.103, G.109, G.110, W.111, H.116, G.135, E.136, L.140, T.153 Ligands: NDG.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.111 Hydrogen bonds: A:N.103, A:N.103, A:G.109, A:W.111, A:E.136 Water bridges: A:A.137

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

NDG.9: 9 residues within 4Å: Chain A: D.159, Q.164, G.165, W.166, H.171, G.190, E.191, F.195 Ligands: NAG.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.166 Hydrogen bonds: A:D.159, A:Q.164, A:Q.164, A:W.166, A:E.191 Water bridges: A:N.192 NDG.15: 10 residues within 4Å: Chain A: N.103, G.109, G.110, W.111, H.116, G.135, E.136, L.140, T.153 Ligands: NAG.14 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:E.136 Water bridges: A:G.109, A:A.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ribeiro, J.P. et al., Biophysical characterization and structural determination of the potent cytotoxic Psathyrella asperospora lectin. Proteins (2017)

Release Date

2017-02-22

Peptides

GlcNAc specific lectin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GlcNAc specific lectin