SMTL ID : 5kxc.1

Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 8.5.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NAG-FUC.1: 3 residues within 4Å: Chain A: R.114, N.116, S.118 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.118

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.2: 4 residues within 4Å: Chain C: H.111, R.114, N.116, S.118 No protein-ligand interaction detected (PLIP)

4 x 6Y2: ~{N}-[(2~{S},3~{R},4~{R},5~{R},6~{R})-2-[(2~{R},3~{S},4~{R},5~{R},6~{S})-5-acetamido-2-(hydroxymethyl)-6-(4-nitrophenoxy)-4-oxidanyl-oxan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]ethanamide(Non-covalent)

6Y2.3: 9 residues within 4Å: Chain A: D.87, G.104, G.105, F.129, N.131, G.214, L.215, S.216, H.219 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.87, A:G.105, A:N.131, A:N.131, A:L.215, A:S.216, A:S.216, A:S.216 6Y2.7: 9 residues within 4Å: Chain B: D.87, G.104, G.105, F.129, N.131, G.214, L.215, S.216, H.219 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.87, B:G.105, B:N.131, B:N.131, B:L.215, B:L.215, B:S.216, B:H.219 6Y2.10: 9 residues within 4Å: Chain C: D.87, G.104, G.105, F.129, N.131, G.214, L.215, S.216, H.219 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.87, C:G.105, C:N.131, C:N.131, C:L.215, C:S.216, C:S.216 6Y2.14: 10 residues within 4Å: Chain D: D.87, G.104, G.105, F.129, N.131, W.133, G.214, L.215, S.216, H.219 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.133 Hydrogen bonds: D:D.87, D:G.105, D:N.131, D:N.131, D:L.215, D:L.215, D:L.215, D:S.216, D:S.216

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.127, F.129, N.131, D.134 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.127, A:D.127, A:F.129, H2O.3, H2O.3 CA.8: 4 residues within 4Å: Chain B: D.127, F.129, N.131, D.134 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.127, B:D.127, B:F.129, B:D.134, H2O.9 CA.11: 4 residues within 4Å: Chain C: D.127, F.129, N.131, D.134 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.127, C:F.129, C:D.134, H2O.14, H2O.16 CA.15: 4 residues within 4Å: Chain D: D.127, F.129, N.131, D.134 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.127, D:D.127, D:F.129, D:D.134, H2O.22

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

MN.5: 4 residues within 4Å: Chain A: E.125, D.127, D.134, H.139 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.125, A:D.127, A:D.134, A:H.139, H2O.1, H2O.2 MN.9: 4 residues within 4Å: Chain B: E.125, D.127, D.134, H.139 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.125, B:D.127, B:D.134, B:H.139, H2O.7, H2O.9 MN.12: 4 residues within 4Å: Chain C: E.125, D.127, D.134, H.139 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.125, C:D.127, C:D.134, C:H.139, H2O.14, H2O.16 MN.16: 4 residues within 4Å: Chain D: E.125, D.127, D.134, H.139 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.125, D:D.127, D:D.134, D:H.139, H2O.20, H2O.20

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

NAG.6: 3 residues within 4Å: Chain B: N.116, S.118, N.119 No protein-ligand interaction detected (PLIP) NAG.13: 4 residues within 4Å: Chain D: R.114, N.116, S.118, N.119 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haji-Ghassemi, O. et al., Molecular Basis for Recognition of the Cancer Glycobiomarker, LacdiNAc (GalNAc[ beta 14]GlcNAc), by Wisteria floribunda Agglutinin. J.Biol.Chem. (2016)

Release Date

2016-09-14

Peptides

Wisteria floribunda agglutinin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Wisteria floribunda agglutinin

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