SMTL ID : 5u38.1

Crystal structure of native lectin from Platypodium elegans seeds (PELa) complexed with Man1-3Man-OMe.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x MMA- MAN: alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranoside(Non-covalent)

MMA-MAN.1: 10 residues within 4Å: Chain A: A.86, D.87, G.106, G.107, F.133, S.138, N.139, G.221, E.222, Q.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.107, A:N.139, A:G.221, A:E.222, A:Q.223, A:Q.223, A:S.138, A:E.222 Water bridges: A:L.108, A:E.222, A:N.137 MMA-MAN.5: 10 residues within 4Å: Chain B: A.86, D.87, G.106, G.107, F.133, S.138, N.139, G.221, E.222, Q.223 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.107, B:N.139, B:G.221, B:E.222, B:Q.223, B:Q.223, B:S.138 Water bridges: B:L.108, B:E.222, B:N.137

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 3 residues within 4Å: Chain A: N.119, S.121, A.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.119 NAG.6: 3 residues within 4Å: Chain B: N.119, S.121, A.122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.119

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 4 residues within 4Å: Chain A: E.129, D.131, D.142, H.147 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.129, A:D.131, A:D.142, A:H.147, H2O.2, H2O.2 MN.7: 4 residues within 4Å: Chain B: E.129, D.131, D.142, H.147 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.129, B:D.131, B:D.142, B:H.147, H2O.13, H2O.13

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.131, F.133, N.139, D.142 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:F.133, A:D.142, H2O.2, H2O.3 CA.8: 4 residues within 4Å: Chain B: D.131, F.133, N.139, D.142 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.131, B:F.133, B:D.142, H2O.13, H2O.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cavada, B.S. et al., Structural studies and nociceptive activity of a native lectin from Platypodium elegans seeds (nPELa). Int. J. Biol. Macromol. (2018)

Release Date

2017-10-04

Peptides

Lectin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Lectin