SMTL ID : 5ava.2 (1 other biounit)

Crystal structure of PHA-E lectin in complex with bisected glycan

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

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

NAG-BMA-MAN-NAG-GAL-MAN-NAG-NAG.1: 16 residues within 4Å: Chain A: D.122, K.123, G.124, G.125, L.126, Y.133, L.149, Y.150, N.151, V.152, H.153, W.154, G.235, I.236, T.237, N.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.150, A:Y.150, A:N.240, A:D.122, A:D.122 NAG-BMA-MAN-NAG-GAL-MAN-NAG-NAG.2: 14 residues within 4Å: Chain B: D.122, K.123, G.124, G.125, L.126, L.149, Y.150, N.151, H.153, W.154, G.235, I.236, T.237, N.240 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.150, B:N.240, B:D.122 NAG-BMA-MAN-NAG-GAL-MAN-NAG-NAG.3: 17 residues within 4Å: Chain C: S.65, D.107, D.122, K.123, G.124, G.125, L.126, L.149, Y.150, N.151, V.152, H.153, W.154, G.235, I.236, T.237, N.240 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.150, C:N.240, C:S.65, C:S.65, C:D.122 NAG-BMA-MAN-NAG-GAL-MAN-NAG-NAG.4: 16 residues within 4Å: Chain D: D.107, D.122, K.123, G.124, G.125, L.126, L.149, Y.150, N.151, V.152, H.153, W.154, G.235, I.236, T.237, N.240 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.240, D:D.122, D:D.122

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

MN.5: 5 residues within 4Å: Chain A: E.145, D.147, D.155, H.160 Ligands: CA.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.147, A:D.155, A:H.160, H2O.1, H2O.1 MN.7: 5 residues within 4Å: Chain B: E.145, D.147, D.155, H.160 Ligands: CA.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.147, B:D.155, B:H.160, H2O.1, H2O.1 MN.9: 5 residues within 4Å: Chain C: E.145, D.147, D.155, H.160 Ligands: CA.10 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.145, C:D.147, C:D.155, C:H.160, H2O.1 MN.11: 4 residues within 4Å: Chain D: E.145, D.147, D.155, H.160 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.147, D:D.155, D:H.160, H2O.1, H2O.1

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.147, L.149, N.151, D.155 Ligands: MN.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.147, A:L.149, A:D.155, H2O.1, H2O.1 CA.8: 5 residues within 4Å: Chain B: D.147, L.149, N.151, D.155 Ligands: MN.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.147, B:L.149, B:D.155, H2O.1, H2O.1 CA.10: 5 residues within 4Å: Chain C: D.147, L.149, N.151, D.155 Ligands: MN.9 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.147, C:L.149, C:D.155, H2O.1, H2O.1 CA.12: 4 residues within 4Å: Chain D: D.147, L.149, N.151, D.155 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.147, D:D.147, D:L.149, D:D.155, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagae, M. et al., Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins. Sci Rep (2016)

Release Date

2016-04-27

Peptides

Erythroagglutinin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Erythroagglutinin

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