SMTL ID : 5kxd.1

Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 6.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

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:N.116 NAG-FUC.3: 4 residues within 4Å: Chain D: R.114, N.116, S.118, N.119 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.116

1 x NAG- NAG- BMA- XYP- MAN- MAN- FUC: beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]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(Non-functional Binders)

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

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.4: 4 residues within 4Å: Chain A: D.127, F.129, N.131, D.134 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.127, A:D.127, A:F.129, A:D.134, H2O.2 CA.9: 4 residues within 4Å: Chain B: D.127, F.129, N.131, D.134 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.127, B:F.129, B:D.134, H2O.10, H2O.11 CA.13: 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.16, H2O.16 CA.18: 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-functional Binders)(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.10: 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.9, H2O.10 MN.14: 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.16, H2O.16 MN.19: 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.21

6 x ACT: ACETATE ION(Non-covalent)(Non-functional Binders)

ACT.6: 2 residues within 4Å: Chain A: F.129 Ligands: 6Y2.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.131, A:S.132 ACT.11: 5 residues within 4Å: Chain B: R.150, V.195, D.196, Q.199, I.200 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.196, B:Q.199 Hydrogen bonds: B:D.196 Salt bridges: B:R.150 ACT.15: 3 residues within 4Å: Chain C: N.131, S.132 Ligands: 6Y2.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.132, C:S.132 ACT.16: 5 residues within 4Å: Chain C: R.150, V.195, D.196, Q.199, I.200 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:D.196, C:Q.199 Hydrogen bonds: C:D.196 Salt bridges: C:R.150 ACT.20: 3 residues within 4Å: Chain D: N.131, S.132 Ligands: 6Y2.22 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.131, D:S.132, D:S.132 Water bridges: D:S.132 ACT.21: 4 residues within 4Å: Chain D: R.150, V.195, D.196, I.200 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:D.196 Hydrogen bonds: D:D.196 Salt bridges: D:R.150

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(Post Translational Modification)(Non-functional Binders)

6Y2.7: 10 residues within 4Å: Chain A: D.87, G.104, G.105, F.129, N.131, G.214, L.215, S.216, H.219 Ligands: ACT.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.87, A:G.105, A:N.131, A:N.131, A:L.215, A:L.215, A:S.216, A:H.219 Water bridges: A:L.106, A:S.216, A:S.216 6Y2.12: 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:S.216 6Y2.17: 10 residues within 4Å: Chain C: D.87, G.104, G.105, F.129, N.131, G.214, L.215, S.216, H.219 Ligands: ACT.15 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:H.219 6Y2.22: 12 residues within 4Å: Chain D: D.87, P.103, G.104, G.105, F.129, N.131, W.133, G.214, L.215, S.216, H.219 Ligands: ACT.20 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

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

NAG.8: 2 residues within 4Å: Chain B: N.116, S.118 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   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