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

Crystal Structure of basic winged bean lectin with Tn-antigen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

3 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: 4 residues within 4Å: Chain A: F.81, P.84, Q.218, N.220 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.3: 5 residues within 4Å: Chain B: F.81, R.83, P.84, Q.218, N.220 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.4: 1 residues within 4Å: Chain B: N.45 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.2: 3 residues within 4Å: Chain A: W.44, N.45, P.214 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.44, A:P.214 Hydrogen bonds: A:N.45 Water bridges: A:R.22

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.9: 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.4, H2O.4

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

MN.6: 4 residues within 4Å: Chain A: E.123, D.125, D.132, H.137 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.123, A:D.125, A:H.137, H2O.1, H2O.1 MN.10: 4 residues within 4Å: Chain B: E.123, D.125, D.132, H.137 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.123, B:D.125, B:D.132, B:H.137, H2O.4, H2O.4

2 x SER: SERINE(Non-functional Binders)(Non-covalent)

SER.7: 1 residues within 4Å: Ligands: A2G.8 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Water bridges: A:T.130 Hydrogen bonds: S.7, S.7 SER.11: 2 residues within 4Å: Chain B: G.216 Ligands: A2G.12 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.130, B:S.215

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

A2G.8: 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.7 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:D.88, A:G.106, A:N.129, A:N.129, A:D.213, S.7 Water bridges: A:S.215, A:G.216, A:Q.218 A2G.12: 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.11 8 PLIP interactions: 7 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.11 Water bridges: B:G.216, B:Q.218

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
A

B
B

Basic agglutinin

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