SMTL ID : 6vc3.1

Peanut lectin complexed with S-beta-D-thiogalactopyranosyl 6-deoxy-6-S-propynyl-beta-D-glucopyranoside (STG)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

3 x QWJ: 6-S-(prop-2-yn-1-yl)-6-thio-beta-D-glucopyranosyl 1-thio-beta-D-galactopyranoside(Non-covalent)

QWJ.1: 11 residues within 4Å: Chain A: D.80, A.82, D.83, G.103, G.104, Y.125, N.127, E.129, S.211, G.213, G.214 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.80, A:D.83, A:G.104, A:Y.125, A:N.127, A:S.211 Water bridges: A:G.102, A:E.129, A:E.129, A:L.212, A:G.214 QWJ.4: 11 residues within 4Å: Chain B: D.80, A.82, D.83, G.103, G.104, Y.125, N.127, E.129, S.211, G.213, G.214 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.83, B:G.104, B:N.127, B:S.211 Water bridges: B:G.102, B:E.129 QWJ.9: 11 residues within 4Å: Chain D: D.80, A.82, D.83, G.103, G.104, Y.125, N.127, E.129, S.211, G.213, G.214 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:D.80, D:D.83, D:G.104, D:N.127, D:S.211 Water bridges: D:D.83, D:G.102, D:E.129, D:L.212, D:G.214

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

MN.2: 4 residues within 4Å: Chain A: E.121, D.123, D.132, H.137 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.123, A:D.132, A:H.137, H2O.1, H2O.2 MN.5: 4 residues within 4Å: Chain B: E.121, D.123, D.132, H.137 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.121, B:D.123, B:D.132, B:H.137, H2O.7, H2O.8 MN.7: 4 residues within 4Å: Chain C: E.121, D.123, D.132, H.137 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.121, C:D.123, C:D.132, C:H.137, H2O.12, H2O.13 MN.10: 4 residues within 4Å: Chain D: E.121, D.123, D.132, H.137 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.121, D:D.123, D:D.132, D:H.137, H2O.16, H2O.18

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.123, Y.125, N.127, D.132 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.123, A:Y.125, A:D.132, H2O.1, H2O.3 CA.6: 4 residues within 4Å: Chain B: D.123, Y.125, N.127, D.132 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.123, B:Y.125, B:D.132, H2O.7, H2O.7 CA.8: 4 residues within 4Å: Chain C: D.123, Y.125, N.127, D.132 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.123, C:Y.125, C:D.132, H2O.13, H2O.13 CA.11: 4 residues within 4Å: Chain D: D.123, Y.125, N.127, D.132 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.123, D:Y.125, D:D.132, H2O.17, H2O.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cagnoni, A.J. et al., Crystal structures of peanut lectin in the presence of synthetic beta-N- and beta-S-galactosides disclose evidence for the recognition of different glycomimetic ligands. Acta Crystallogr D Struct Biol (2020)

Release Date

2020-10-28

Peptides

Galactose-binding lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Galactose-binding lectin

Related Entries With Identical Sequence