SMTL ID : 2zmk.2 (5 other biounits)

Crystl structure of Basic Winged bean lectin in complex with Gal-alpha-1,4-Gal-Beta-Ethylene

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x EGA- GLA: alpha-D-galactopyranose-(1-4)-ethyl beta-D-galactopyranoside(Non-covalent)

EGA-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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.84, A:D.87, A:G.105, A:N.128, A:N.128, A:D.212, A:G.215 EGA-GLA.5: 12 residues within 4Å: Chain B: H.84, D.87, G.104, G.105, F.126, N.128, T.129, G.211, D.212, S.214, G.215, A.220 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.129 Hydrogen bonds: B:S.214, B:D.87, B:G.105, B:N.128, B:N.128, B:D.212, B:G.215

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

NAG-FUC.2: 2 residues within 4Å: Chain A: N.44, P.213 No protein-ligand interaction detected (PLIP) NAG-FUC.3: 3 residues within 4Å: Chain B: F.80, R.82, N.219 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.79

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(Post Translational Modification)

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

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

MN.6: 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.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.2

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 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.11: 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.2

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

NAG.8: 5 residues within 4Å: Chain A: F.80, R.82, P.83, Q.217, N.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.79, A:N.219

1 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   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
C

B
D

Basic agglutinin

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