SMTL ID : 2d3s.2 (1 other biounit)

Crystal Structure of basic winged bean lectin with Tn-antigen

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 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: 5 residues within 4Å: Chain A: F.81, R.83, P.84, Q.218, N.220 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(Post Translational Modification)

NAG-FUC-NAG.2: 4 residues within 4Å: Chain B: R.22, W.44, N.45, P.214 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: R.22, N.45, P.214 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.214 Hydrogen bonds: A:R.22, A:N.45

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.125, F.127, N.129, D.132 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.125, A:F.127, A:D.132, H2O.1, H2O.1 CA.8: 4 residues within 4Å: Chain B: D.125, F.127, N.129, D.132 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:F.127, B:D.132, H2O.3, H2O.3

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

MN.5: 4 residues within 4Å: Chain A: E.123, D.125, D.132, H.137 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.123, A:D.125, A:D.132, A:H.137, H2O.1 MN.9: 4 residues within 4Å: Chain B: E.123, D.125, D.132, H.137 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.123, B:D.132, B:H.137, H2O.3, H2O.3

2 x SER: SERINE(Non-covalent)

SER.6: 3 residues within 4Å: Chain A: F.127, G.216 Ligands: A2G.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Water bridges: A:T.130, S.6, S.6 SER.10: 2 residues within 4Å: Chain B: G.216 Ligands: A2G.11 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Ligand interactions Water bridges: B:T.130, B:S.215, S.10, S.10 Hydrogen bonds: S.10, S.10

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

A2G.7: 12 residues within 4Å: Chain A: H.85, D.88, G.105, G.106, F.127, N.129, G.212, D.213, S.215, G.216, A.221 Ligands: SER.6 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:H.85, A:D.88, A:G.106, A:N.129, A:N.129, A:D.213, S.6 Water bridges: A:G.216, A:G.216 A2G.11: 12 residues within 4Å: Chain B: H.85, D.88, G.105, G.106, F.127, N.129, G.212, D.213, S.215, G.216, A.221 Ligands: SER.10 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:D.88, B:G.106, B:N.129, B:N.129, B:D.213, S.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kulkarni, K.A. et al., Structural basis for the specificity of basic winged bean lectin for the Tn-antigen: a crystallographic, thermodynamic and modelling study. Febs Lett. (2005)

Release Date

2006-01-17

Peptides

Basic agglutinin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Basic agglutinin

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