SMTL ID : 1g9f.1

CRYSTAL STRUCTURE OF THE SOYBEAN AGGLUTININ IN A COMPLEX WITH A BIANTENNARY BLOOD GROUP ANTIGEN ANALOG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: N.9, K.31, N.75, V.161, P.182, L.224, S.225 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.31, A:L.224 NAG-NAG.5: 7 residues within 4Å: Chain B: N.9, K.31, N.75, V.161, P.182, L.224, S.225 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.31, B:L.224 NAG-NAG.9: 7 residues within 4Å: Chain C: N.9, K.31, N.75, V.161, P.182, L.224, S.225 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.31, C:L.224 NAG-NAG.13: 7 residues within 4Å: Chain D: N.9, K.31, N.75, V.161, P.182, L.224, S.225 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.31, D:L.224

4 x GAL- NAG- GAL- NAG- GAL: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]beta-D-galactopyranose

GAL-NAG-GAL-NAG-GAL.2: 8 residues within 4Å: Chain A: D.88, G.106, F.128, N.130, G.213, L.214, D.215, I.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.215, A:D.88, A:G.106, A:N.130, A:N.130, A:L.214 GAL-NAG-GAL-NAG-GAL.6: 9 residues within 4Å: Chain A: P.135 Chain B: D.88, G.106, F.128, N.130, G.213, L.214, D.215, I.216 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.215, B:D.88, B:G.106, B:N.130, B:N.130, B:L.214 GAL-NAG-GAL-NAG-GAL.10: 8 residues within 4Å: Chain C: D.88, G.106, F.128, N.130, G.213, L.214, D.215, I.216 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.215, C:D.88, C:G.106, C:N.130, C:N.130, C:L.214 GAL-NAG-GAL-NAG-GAL.14: 9 residues within 4Å: Chain C: P.135 Chain D: D.88, G.106, F.128, N.130, G.213, L.214, D.215, I.216 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.215, D:D.88, D:G.106, D:N.130, D:N.130, D:L.214

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

MN.3: 5 residues within 4Å: Chain A: E.124, D.126, D.133, H.138 Ligands: CA.4 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.124, A:D.126, A:D.133, A:H.138, H2O.1, H2O.1 MN.7: 5 residues within 4Å: Chain B: E.124, D.126, D.133, H.138 Ligands: CA.8 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.124, B:D.126, B:D.133, B:H.138, H2O.1, H2O.1 MN.11: 5 residues within 4Å: Chain C: E.124, D.126, D.133, H.138 Ligands: CA.12 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.124, C:D.126, C:D.133, C:H.138, H2O.1, H2O.1 MN.15: 5 residues within 4Å: Chain D: E.124, D.126, D.133, H.138 Ligands: CA.16 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.124, D:D.126, D:D.133, D:H.138, H2O.2, H2O.2

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.126, F.128, N.130, D.133 Ligands: MN.3 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: 5 residues within 4Å: Chain B: D.126, F.128, N.130, D.133 Ligands: MN.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.126, B:F.128, B:D.133, H2O.1, H2O.1 CA.12: 5 residues within 4Å: Chain C: D.126, F.128, N.130, D.133 Ligands: MN.11 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.126, C:F.128, C:D.133, H2O.1, H2O.1 CA.16: 5 residues within 4Å: Chain D: D.126, F.128, N.130, D.133 Ligands: MN.15 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.126, D:F.128, D:D.133, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buts, L. et al., Weak protein-protein interactions in lectins: the crystal structure of a vegetative lectin from the legume Dolichos biflorus. J.Mol.Biol. (2001)

Release Date

2001-06-13

Peptides

LECTIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

LECTIN

Related Entries With Identical Sequence