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

Crystal Structure of basic winged bean lectin in complex with 2Me-O-D-Galactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA-FUC.1: 4 residues within 4Å: Chain A: F.80, P.83, Q.217, N.219 No protein-ligand interaction detected (PLIP)

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

NAG-FUL-NAG.2: 3 residues within 4Å: Chain A: R.21, N.44, P.213 No protein-ligand interaction detected (PLIP)

1 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.3: 2 residues within 4Å: Chain B: R.21, N.44 No protein-ligand interaction detected (PLIP)

2 x 2GS: 2-O-methyl-alpha-D-galactopyranose(Non-covalent)

2GS.4: 10 residues within 4Å: Chain A: H.84, D.87, G.104, G.105, F.126, N.128, G.211, D.212, G.215, A.220 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.87, A:G.105, A:N.128, A:N.128, A:D.212 Water bridges: A:G.215, A:Q.217 2GS.7: 10 residues within 4Å: Chain B: H.84, D.87, G.104, G.105, F.126, N.128, G.211, D.212, G.215, A.220 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.87, B:G.105, B:N.128, B:N.128, B:D.212

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.2, H2O.2 CA.9: 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.5, H2O.5

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

MN.6: 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.2, H2O.2 MN.10: 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.5, H2O.5

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

NAG.8: 4 residues within 4Å: Chain B: F.80, P.83, Q.217, N.219 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.83 Hydrogen bonds: B:N.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kulkarni, K.A. et al., Structural basis for the carbohydrate-specificity of basic winged-bean lectin and its differential affinity for Gal and GalNAc. ACTA CRYSTALLOGR.,SECT.D (2006)

Release Date

2006-11-07

Peptides

Basic agglutinin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Basic agglutinin

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