SMTL ID : 1sbe.1

SOYBEAN AGGLUTININ FROM GLYCINE MAX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.88, A:G.106, A:N.130, A:N.130, A:L.214, A:D.215 NAG-GAL.5: 9 residues within 4Å: Chain B: D.88, A.105, G.106, F.128, N.130, G.213, L.214, D.215, I.216 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.88, B:G.106, B:N.130, B:N.130, B:L.214, B:D.215 NAG-GAL.9: 9 residues within 4Å: Chain C: D.88, A.105, G.106, F.128, N.130, G.213, L.214, D.215, I.216 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.88, C:G.106, C:N.130, C:N.130, C:L.214, C:D.215 NAG-GAL.13: 9 residues within 4Å: Chain D: D.88, A.105, G.106, F.128, N.130, G.213, L.214, D.215, I.216 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.88, D:G.106, D:N.130, D:N.130, D:L.214, D:D.215

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

NAG.2: 6 residues within 4Å: Chain A: N.9, N.75, V.161, P.182, L.224, S.225 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.182 Hydrogen bonds: A:N.9, A:N.75, A:S.225 NAG.6: 6 residues within 4Å: Chain B: N.9, N.75, V.161, P.182, L.224, S.225 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.182 Hydrogen bonds: B:N.9, B:N.75, B:S.225 NAG.10: 6 residues within 4Å: Chain C: N.9, N.75, V.161, P.182, L.224, S.225 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:P.182 Hydrogen bonds: C:N.9, C:N.75, C:S.225 NAG.14: 6 residues within 4Å: Chain D: N.9, N.75, V.161, P.182, L.224, S.225 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:P.182 Hydrogen bonds: D:N.9, D:N.75, D:S.225

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

MN.3: 5 residues within 4Å: Chain A: E.124, D.126, D.133, H.138, S.148 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.124, A:D.126, A:H.138, H2O.1, H2O.1 MN.7: 5 residues within 4Å: Chain B: E.124, D.126, D.133, H.138, S.148 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.124, B:D.126, B:H.138, H2O.2, H2O.2 MN.11: 5 residues within 4Å: Chain C: E.124, D.126, D.133, H.138, S.148 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.124, C:D.126, C:H.138, H2O.2, H2O.2 MN.15: 5 residues within 4Å: Chain D: E.124, D.126, D.133, H.138, S.148 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.124, D:D.126, D:H.138, H2O.3, H2O.3

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.8: 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.2, H2O.2 CA.12: 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.2, H2O.2 CA.16: 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.3, H2O.3

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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