SMTL ID : 2e51.1 (1 other biounit)

Crystal structure of basic winged bean lectin in complex with A blood group disaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x GLA- A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-alpha-D-galactopyranose(Non-covalent)

GLA-A2G.1: 12 residues within 4Å: Chain A: H.84, D.87, G.104, G.105, Y.106, F.126, N.128, G.211, D.212, S.214, G.215, A.220 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.106 Hydrogen bonds: A:D.87, A:G.105, A:N.128, A:N.128, A:D.212, A:S.214 Water bridges: A:Q.217, A:Q.217 GLA-A2G.4: 12 residues within 4Å: Chain B: H.84, D.87, G.104, G.105, Y.106, F.126, N.128, G.211, D.212, S.214, G.215, A.220 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.106 Hydrogen bonds: B:D.87, B:G.105, B:N.128, B:N.128, B:D.212, B:S.214, B:S.214 Water bridges: B:G.215, B:Q.217

4 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.2: 5 residues within 4Å: Chain A: F.80, R.82, P.83, Q.217, N.219 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.3: 2 residues within 4Å: Chain A: N.44, P.213 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.5: 4 residues within 4Å: Chain B: F.80, R.82, P.83, N.219 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.6: 3 residues within 4Å: Chain B: W.43, N.44, P.213 No protein-ligand interaction detected (PLIP)

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

MN.7: 4 residues within 4Å: Chain A: E.122, D.124, D.131, H.136 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.122, A:D.124, A:D.131, A:H.136, H2O.2 MN.9: 4 residues within 4Å: Chain B: E.122, D.124, D.131, H.136 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.122, B:D.124, B:D.131, B:H.136, H2O.4, H2O.5

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 4 residues within 4Å: Chain A: D.124, F.126, N.128, D.131 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.124, A:D.124, A:F.126, A:D.131, H2O.2 CA.10: 4 residues within 4Å: Chain B: D.124, F.126, N.128, D.131 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.124, B:F.126, B:D.131, H2O.4, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kulkarni, K.A. et al., Generation of blood group specificity: new insights from structural studies on the complexes of A- and B-reactive saccharides with basic winged bean agglutinin. Proteins (2007)

Release Date

2007-06-26

Peptides

Basic agglutinin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Basic agglutinin

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