SMTL ID : 2du1.2 (1 other biounit)

Crystal Structure of basic winged bean lectin in complex with Methyl-alpha-N-acetyl-D galactosamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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.1: 5 residues within 4Å: Chain A: F.80, R.82, P.83, Q.217, N.219 No protein-ligand interaction detected (PLIP)

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

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

2 x MGC: methyl 2-acetamido-2-deoxy-alpha-D-galactopyranoside(Non-covalent)

MGC.3: 12 residues within 4Å: Chain A: H.84, D.87, G.104, G.105, F.126, N.128, W.130, G.211, D.212, S.214, G.215, A.220 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.130 Hydrogen bonds: A:H.84, A:G.105, A:N.128, A:N.128, A:D.212 Water bridges: A:G.215 MGC.7: 13 residues within 4Å: Chain B: H.84, D.87, G.104, G.105, Y.106, F.126, N.128, W.130, G.211, D.212, S.214, G.215, A.220 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.106, B:W.130 Hydrogen bonds: B:G.105, B:N.128, B:N.128, B:D.212

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

NAG.4: 2 residues within 4Å: Chain A: R.21, N.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.21, A:N.44 NAG.8: 5 residues within 4Å: Chain B: F.80, R.82, P.83, Q.217, N.219 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.83 Hydrogen bonds: B:N.219

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.1, H2O.1 CA.9: 4 residues within 4Å: Chain B: D.124, F.126, N.128, D.131 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.124, B:D.124, B:F.126, B:D.131, H2O.3

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

MN.6: 5 residues within 4Å: Chain A: E.122, D.124, D.131, H.136, V.144 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.1 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.2, H2O.3

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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