SMTL ID : 5xfi.1

Crystal structure of Calsepa lectin in complex with biantennary N-glycan

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- 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-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1: 15 residues within 4Å: Chain A: G.16, G.17, N.18, G.64, L.94, D.95, N.96, G.140, Y.141, Y.142, D.144 Chain B: V.25, R.151 Ligands: EDO.5, BEZ.6 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.96, A:N.96, B:V.25, B:R.151, A:N.18 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.2: 15 residues within 4Å: Chain A: V.25, R.151 Chain B: G.16, G.17, N.18, G.64, L.94, D.95, N.96, G.140, Y.141, Y.142, D.144 Ligands: EDO.9, BEZ.10 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.96, B:N.96, B:N.18, A:V.25, A:R.151

4 x SO4: SULFATE ION(Non-covalent)(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: K.27, T.79, D.80, E.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.80 Salt bridges: A:K.27 SO4.4: 3 residues within 4Å: Chain A: W.12, G.13, F.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.13 SO4.7: 5 residues within 4Å: Chain B: K.27, G.78, T.79, D.80, E.81 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.80, B:E.81 Water bridges: B:K.27 Salt bridges: B:K.27 SO4.8: 3 residues within 4Å: Chain B: W.12, G.13, F.122 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.13, B:G.13 Water bridges: B:P.121

2 x EDO: 1,2-ETHANEDIOL(Non-covalent)(Non-functional Binders)

EDO.5: 3 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.2, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.2, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.2 No protein-ligand interaction detected (PLIP)

2 x BEZ: BENZOIC ACID(Non-covalent)(Non-functional Binders)

BEZ.6: 5 residues within 4Å: Chain A: Y.141 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1 No protein-ligand interaction detected (PLIP) BEZ.10: 5 residues within 4Å: Chain B: Y.141 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.2, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.2, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.2, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Nagae, M. et al., Distinct roles for each N-glycan branch interacting with mannose-binding type Jacalin-related lectins Orysata and Calsepa. Glycobiology (2017)

Release Date

2017-10-18

Peptides

Lectin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lectin