SMTL ID : 3ca5.2 (3 other biounits)

Crystal structure of Sambucus nigra agglutinin II (SNA-II)-tetragonal crystal form- complexed to alpha1 methylgalactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

NAG-FUC-NAG.1: 3 residues within 4Å: Chain A: N.63, E.113, D.114 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.2: 6 residues within 4Å: Chain A: G.53, K.54, N.71, S.73, T.74 Ligands: SO4.9 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.13: 3 residues within 4Å: Chain B: N.63, E.113, D.114 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.14: 6 residues within 4Å: Chain B: G.53, K.54, N.71, S.73, T.74 Ligands: SO4.21 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 6 residues within 4Å: Chain A: V.133, Q.166, N.178, R.181, L.256, P.257 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.181 NAG-NAG.15: 6 residues within 4Å: Chain B: V.133, Q.166, N.178, R.181, L.256, P.257 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.181

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

NAG.4: 3 residues within 4Å: Chain A: N.232, S.234, L.235 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.232 NAG.16: 3 residues within 4Å: Chain B: N.232, S.234, L.235 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.232

4 x AMG: methyl alpha-D-galactopyranoside(Non-covalent)

AMG.5: 10 residues within 4Å: Chain A: D.16, V.17, R.18, N.19, G.20, Q.29, W.31, Q.36, N.38, R.107 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.16, A:N.19, A:G.20, A:Q.29, A:Q.29, A:Q.36, A:N.38 Water bridges: A:R.107 AMG.6: 7 residues within 4Å: Chain A: D.227, V.228, R.229, A.230, I.239, F.241, N.248 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.227, A:A.230, A:N.248, A:N.248 Water bridges: A:K.193, A:R.229, A:R.229, A:N.246 AMG.17: 10 residues within 4Å: Chain B: D.16, V.17, R.18, N.19, G.20, Q.29, W.31, Q.36, N.38, R.107 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.16, B:N.19, B:G.20, B:Q.29, B:Q.29, B:Q.36, B:N.38 Water bridges: B:R.107 AMG.18: 7 residues within 4Å: Chain B: D.227, V.228, R.229, A.230, I.239, F.241, N.248 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.227, B:A.230, B:N.248, B:N.248 Water bridges: B:K.193, B:R.229, B:R.229, B:N.246

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 2 residues within 4Å: Chain A: A.76, E.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.77 SO4.8: 3 residues within 4Å: Chain A: T.4, R.37, R.40 8 PLIP interactions: 8 interactions with chain A Water bridges: A:T.4, A:T.4, A:R.5, A:R.37, A:R.37, A:R.40 Salt bridges: A:R.37, A:R.40 SO4.9: 5 residues within 4Å: Chain A: N.71, C.72, S.73 Ligands: NAG-FUC-NAG.2, NAG-FUC-NAG.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.71, A:C.72, A:S.73, A:S.73 Water bridges: A:R.50, A:R.50 SO4.10: 8 residues within 4Å: Chain A: S.162, L.163, Q.164 Chain B: T.161, S.162, L.163, Q.164 Ligands: SO4.22 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.163, A:Q.164, B:L.163, B:Q.164 SO4.11: 3 residues within 4Å: Chain A: R.18, N.19, R.107 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.19, A:N.19 Water bridges: A:R.107, A:R.107 Salt bridges: A:R.18, A:R.107 SO4.19: 2 residues within 4Å: Chain B: A.76, E.77 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.77 SO4.20: 3 residues within 4Å: Chain B: T.4, R.37, R.40 7 PLIP interactions: 7 interactions with chain B Water bridges: B:T.4, B:R.5, B:R.37, B:R.37, B:R.40 Salt bridges: B:R.37, B:R.40 SO4.21: 5 residues within 4Å: Chain B: N.71, C.72, S.73 Ligands: NAG-FUC-NAG.14, NAG-FUC-NAG.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.71, B:C.72, B:S.73, B:S.73 Water bridges: B:R.50, B:R.50 SO4.22: 8 residues within 4Å: Chain A: T.161, S.162, L.163, Q.164 Chain B: S.162, L.163, Q.164 Ligands: SO4.10 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.163, A:Q.164, B:L.163, B:Q.164 SO4.23: 3 residues within 4Å: Chain B: R.18, N.19, R.107 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.19, B:N.19 Water bridges: B:R.107, B:R.107 Salt bridges: B:R.18, B:R.107

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 1 residues within 4Å: Chain A: N.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.59 ACT.24: 1 residues within 4Å: Chain B: N.59 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maveyraud, L. et al., Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra. Proteins (2009)

Release Date

2008-11-25

Peptides

Agglutinin II: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Agglutinin II

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