SMTL ID : 2arx.1

Pterocarpus angolensis seed lectin in complex with the decasaccharide NA2F

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

1 x MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.1: 11 residues within 4Å: Chain A: A.85, D.86, G.105, G.106, F.132, D.136, S.137, N.138, G.220, E.221, Q.222 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.106, A:N.138, A:N.138, A:G.220, A:E.221, A:Q.222, A:Q.222 Water bridges: A:G.104, A:G.220

1 x NDG- BMA- MAN- NAG- GAL- MAN- NAG: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose

NDG-BMA-MAN-NAG-GAL-MAN-NAG.2: 16 residues within 4Å: Chain B: S.45, N.83, A.85, D.86, G.104, G.105, G.106, L.107, F.132, A.134, D.136, S.137, N.138, G.220, E.221, Q.222 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.106, B:N.138, B:N.138, B:G.220, B:E.221, B:Q.222, B:Q.222, B:D.136, B:Q.222, B:Q.222, B:G.104, B:E.221, B:E.221 Hydrophobic interactions: B:L.107

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

MN.3: 4 residues within 4Å: Chain A: E.128, D.130, D.141, H.146 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.128, A:D.130, A:D.141, A:H.146, H2O.1, H2O.1 MN.6: 4 residues within 4Å: Chain B: E.128, D.130, D.141, H.146 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.128, B:D.130, B:D.141, B:H.146, H2O.4, H2O.4

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.130, F.132, N.138, D.141 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.130, A:F.132, A:D.141, H2O.1, H2O.1 CA.7: 4 residues within 4Å: Chain B: D.130, F.132, N.138, D.141 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.130, B:F.132, B:D.141, H2O.4, H2O.4

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

NAG.5: 2 residues within 4Å: Chain B: N.118, A.121 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buts, L. et al., Structural basis for the recognition of complex-type biantennary oligosaccharides by Pterocarpus angolensis lectin. Febs J. (2006)

Release Date

2006-08-01

Peptides

lectin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

lectin

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