SMTL ID : 2zml.1 (5 other biounits)

Crystal structure of basic winged bean lectin in complex with Gal-ALPHA 1,4 Gal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

2 x GLA- GLA: alpha-D-galactopyranose-(1-4)-alpha-D-galactopyranose(Non-covalent)(Post Translational Modification)

GLA-GLA.1: 11 residues within 4Å: Chain A: H.84, D.87, G.104, G.105, F.126, N.128, G.211, D.212, S.214, G.215, A.220 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.84, A:D.87, A:G.105, A:N.128, A:D.212 Water bridges: A:G.215 GLA-GLA.3: 11 residues within 4Å: Chain B: H.84, D.87, G.104, G.105, F.126, N.128, G.211, D.212, S.214, G.215, A.220 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.87, B:G.105, B:N.128, B:N.128, B:D.212 Water bridges: B:G.215, B:Q.217

2 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(Non-covalent)

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.4: 4 residues within 4Å: Chain B: F.80, R.82, P.83, N.219 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.5: 2 residues within 4Å: Chain B: N.44, P.213 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.213 Hydrogen bonds: B:N.44

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

NAG.6: 2 residues within 4Å: Chain A: N.44, P.213 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.213 Hydrogen bonds: A:N.44 Water bridges: A:R.21, A:R.21, A:D.22

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

MN.7: 4 residues within 4Å: Chain A: E.122, D.124, D.131, H.136 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.122, A:D.124, A:D.131, A:H.136, H2O.1, H2O.1 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.3, H2O.3

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: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.124, A:F.126, A:D.131, H2O.1, H2O.1 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.3, H2O.3

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Kulkarni, K.A. et al., Structure and sugar-specificity of basic winged-bean lectin: structures of new disaccharide complexes and a comparative study with other known disaccharide complexes of the lectin. Acta Crystallogr.,Sect.D (2008)

Release Date

2008-07-29

Peptides

Basic agglutinin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Basic agglutinin

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