SMTL ID : 1sbd.1

SOYBEAN AGGLUTININ COMPLEXED WITH 2,4-PENTASACCHARIDE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- GAL: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-GAL.1: 9 residues within 4Å: Chain A: D.88, A.105, G.106, F.128, N.130, G.213, L.214, D.215, I.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.88, A:G.106, A:N.130, A:L.214, A:D.215, A:D.215 Water bridges: A:Y.107 Hydrophobic interactions: A:D.215 NAG-GAL.4: 9 residues within 4Å: Chain B: D.88, A.105, G.106, F.128, N.130, G.213, L.214, D.215, I.216 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.88, B:G.106, B:N.130, B:L.214, B:D.215, B:D.215 Water bridges: B:Y.107 Hydrophobic interactions: B:D.215 NAG-GAL.7: 9 residues within 4Å: Chain C: D.88, A.105, G.106, F.128, N.130, G.213, L.214, D.215, I.216 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.88, C:G.106, C:N.130, C:L.214, C:D.215, C:D.215 Water bridges: C:Y.107 Hydrophobic interactions: C:D.215 NAG-GAL.10: 9 residues within 4Å: Chain D: D.88, A.105, G.106, F.128, N.130, G.213, L.214, D.215, I.216 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.88, D:G.106, D:N.130, D:L.214, D:D.215, D:D.215 Water bridges: D:Y.107 Hydrophobic interactions: D:D.215

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

MN.2: 4 residues within 4Å: Chain A: E.124, D.126, D.133, H.138 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.126, A:D.133, A:H.138, H2O.1, H2O.1 MN.5: 4 residues within 4Å: Chain B: E.124, D.126, D.133, H.138 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.126, B:D.133, B:H.138, H2O.2, H2O.3 MN.8: 4 residues within 4Å: Chain C: E.124, D.126, D.133, H.138 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.126, C:D.133, C:H.138, H2O.4, H2O.4 MN.11: 4 residues within 4Å: Chain D: E.124, D.126, D.133, H.138 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.126, D:D.133, D:H.138, H2O.6, H2O.6

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.126, F.128, N.130, D.133 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.126, A:F.128, A:D.133, H2O.1, H2O.1 CA.6: 4 residues within 4Å: Chain B: D.126, F.128, N.130, D.133 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.126, B:F.128, B:D.133, H2O.3, H2O.3 CA.9: 4 residues within 4Å: Chain C: D.126, F.128, N.130, D.133 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.126, C:F.128, C:D.133, H2O.4, H2O.5 CA.12: 4 residues within 4Å: Chain D: D.126, F.128, N.130, D.133 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.126, D:F.128, D:D.133, H2O.6, H2O.6

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Olsen, L.R. et al., X-ray crystallographic studies of unique cross-linked lattices between four isomeric biantennary oligosaccharides and soybean agglutinin. Biochemistry (1997)

Release Date

1998-04-22

Peptides

SOYBEAN AGGLUTININ: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

SOYBEAN AGGLUTININ

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