SMTL ID : 6vav.1

Peanut lectin complexed with divalent N-beta-D-galactopyranosyl-L-succinamoyl derivative (diNGS)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x QTY: N-[[1-[(3S,3aR,6S,6aR)-6-[4-[[[4-[[(2R,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]amino]-4-oxidanylidene-butanoyl]amino]methyl]-1,2,3-triazol-1-yl]-2,3,3a,5,6,6a-hexahydrofuro[3,2-b]furan-3-yl]-1,2,3-triazol-4-yl]methyl]-N'-[(2R,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]butanediamide(Non-covalent)

QTY.1: 12 residues within 4Å: Chain A: D.80, A.82, D.83, G.103, G.104, Y.125, N.127, E.129, S.211, L.212, G.213, G.214 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:D.80, A:D.83, A:G.104, A:N.127, A:E.129, A:S.211, A:S.211 Water bridges: A:G.102, A:Y.125, A:Y.125, A:Y.125, A:Y.125, A:E.129, A:L.212, A:G.213, A:G.214 QTY.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 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.83, B:G.104, B:N.127, B:E.129, B:S.211 Water bridges: B:D.80, B:G.102, B:Y.125, B:Y.125, B:E.129, B:L.212, B:G.213 QTY.7: 12 residues within 4Å: Chain C: D.80, A.82, D.83, G.103, G.104, Y.125, N.127, E.129, S.211, L.212, G.213, G.214 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:D.83, C:G.104, C:N.127, C:E.129, C:S.211 Water bridges: C:G.102, C:Y.125, C:Y.125, C:E.129, C:L.212, C:G.213, C:G.214 QTY.8: 12 residues within 4Å: Chain D: D.80, A.82, D.83, G.103, G.104, Y.125, N.127, E.129, S.211, L.212, G.213, G.214 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:D.80, D:D.83, D:G.104, D:N.127, D:E.129, D:S.211 Water bridges: D:D.80, D:G.102, D:Y.125, D:E.129, D:L.212, D:G.213, D:G.214

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

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.1 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.10 MN.9: 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.30, H2O.31

3 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.3, H2O.5 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.13, H2O.15 CA.10: 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.31

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

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