SMTL ID : 6vgf.1

Peanut lectin complexed with divalent S-beta-D-thiogalactopyranosyl beta-D-glucopyranoside derivative (diSTGD)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-tetramer

Ligands

4 x WA3: (2S,3R,4S,5R,6S)-2-(hydroxymethyl)-6-{[(2S,3R,4S,5S,6S)-3,4,5-trihydroxy-6-({[(1-{[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-({4-[({[(2S,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]sulfanyl}tetrahydro-2H-pyran-2-yl]methyl}sulfanyl)methyl]-1H-1,2,3-triazol-1-yl}methyl)tetrahydro-2H-pyran-2-yl]oxy}tetrahydro-2H-pyran-2-yl]methyl}-1H-1,2,3-triazol-4-yl)methyl]sulfanyl}methyl)tetrahydro-2H-pyran-2-yl]sulfanyl}tetrahydro-2H-pyran-3,4,5-triol

WA3.1: 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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.80, A:D.83, A:G.104, A:N.127, A:S.211, A:S.211 Water bridges: A:E.129, A:E.129, A:G.214 WA3.4: 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, B:S.211 Water bridges: B:G.214 WA3.7: 11 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:D.83, C:G.104, C:S.211, C:S.211 Water bridges: C:E.129, C:G.214 WA3.10: 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 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:D.80, D:D.83, D:G.104, D:N.127, D:S.211, D:S.211 Water bridges: D:Y.125, D:L.212, D:G.214

4 x MN: MANGANESE (II) ION

MN.2: 4 residues within 4Å: Chain A: E.121, D.123, D.132, H.137 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.121, A:D.123, A:D.132, A:H.137, H2O.1, H2O.3 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.10, H2O.11 MN.8: 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.21, H2O.22 MN.11: 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.28, H2O.28

4 x CA: CALCIUM ION

CA.3: 4 residues within 4Å: Chain A: D.123, Y.125, N.127, D.132 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.123, A:D.123, A:Y.125, A:D.132, 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.12, H2O.13 CA.9: 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.21, H2O.21 CA.12: 4 residues within 4Å: Chain D: D.123, Y.125, N.127, D.132 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.123, D:D.123, D:Y.125, D:D.132, H2O.29

Links

RCSB   PDBe   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

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