SMTL ID : 1dbn.1

MAACKIA AMURENSIS LEUKOAGGLUTININ (LECTIN) WITH SIALYLLACTOSE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

2 x BGC- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Post Translational Modification)

BGC-GAL-SIA.1: 11 residues within 4Å: Chain A: Y.45, D.87, S.104, S.106, K.107, Y.131, Y.136, D.137, G.220, Y.221, E.224 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.131, A:E.224, A:E.224, A:Y.45, A:Y.45, A:D.137, A:S.104, A:S.106, A:K.107 Water bridges: A:E.224, A:E.224, A:S.86 Hydrophobic interactions: A:Y.45 Salt bridges: A:K.107 BGC-GAL-SIA.2: 12 residues within 4Å: Chain B: Y.45, D.87, S.104, V.105, S.106, K.107, Y.131, Y.136, D.137, G.220, Y.221, E.224 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.224, B:E.224, B:Y.45, B:D.137, B:S.104, B:S.104, B:S.104, B:S.106, B:K.107 Water bridges: B:Y.221, B:S.86 Hydrophobic interactions: B:Y.45 Salt bridges: B:K.107

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

NAG.3: 1 residues within 4Å: Chain A: N.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.61 NAG.4: 2 residues within 4Å: Chain A: S.102, N.113 No protein-ligand interaction detected (PLIP) NAG.5: 5 residues within 4Å: Chain A: P.178, N.179 Chain B: V.168, F.170, P.189 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.179 Hydrophobic interactions: B:V.168, B:F.170, B:P.189 NAG.8: 3 residues within 4Å: Chain B: P.101, S.102, N.113 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.102, B:S.102 NAG.9: 5 residues within 4Å: Chain A: V.168, F.170, P.189 Chain B: P.178, N.179 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.168, A:F.170, A:P.189 Hydrogen bonds: B:N.179

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: D.129, Y.131, D.137, D.140 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.131, A:D.137, A:D.140, H2O.1, H2O.1 CA.10: 4 residues within 4Å: Chain B: D.129, Y.131, D.137, D.140 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Y.131, B:D.137, B:D.140, H2O.1, H2O.1

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

MN.7: 4 residues within 4Å: Chain A: E.127, D.129, D.140, H.145 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.129, A:D.140, A:H.145, H2O.1, H2O.1 MN.11: 5 residues within 4Å: Chain B: E.127, D.129, D.140, H.145, S.155 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.127, B:D.129, B:D.140, B:H.145, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imberty, A. et al., An unusual carbohydrate binding site revealed by the structures of two Maackia amurensis lectins complexed with sialic acid-containing oligosaccharides. J.Biol.Chem. (2000)

Release Date

2000-06-14

Peptides

PROTEIN (LEUKOAGGLUTININ): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTEIN (LEUKOAGGLUTININ)