SMTL ID : 3ca6.4 (3 other biounits)

Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to Tn antigen

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 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: 5 residues within 4Å: Chain A: G.53, K.54, N.71, S.73, T.74 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.12: 3 residues within 4Å: Chain B: N.63, E.113, D.114 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.13: 5 residues within 4Å: Chain B: G.53, K.54, N.71, S.73, T.74 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.14: 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.15: 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

2 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.5: 11 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 Ligands: SER.11 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Q.36 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:Q.36, A:R.107, S.11 A2G.16: 11 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 Ligands: SER.22 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Q.36 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:Q.36, B:R.107

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

SO4.6: 3 residues within 4Å: Chain A: T.4, R.37, R.40 7 PLIP interactions: 7 interactions with chain A Water bridges: A:T.4, A:T.4, A:T.4, A:T.4, A:T.4 Salt bridges: A:R.37, A:R.40 SO4.7: 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 SO4.8: 3 residues within 4Å: Chain A: S.162, L.163, Q.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.163, A:Q.164 Water bridges: A:Q.145 SO4.9: 3 residues within 4Å: Chain A: W.31, Q.36 Ligands: SER.11 5 PLIP interactions: 3 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: S.11, S.11, S.11 Water bridges: A:Q.36, A:Q.36 SO4.17: 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:T.4, B:T.4, B:T.4, B:T.4 Salt bridges: B:R.37, B:R.40 SO4.18: 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 SO4.19: 3 residues within 4Å: Chain B: S.162, L.163, Q.164 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.163, B:Q.164 Water bridges: B:Q.145 SO4.20: 3 residues within 4Å: Chain B: W.31, Q.36 Ligands: SER.22 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.36, B:Q.36

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

ACT.10: 7 residues within 4Å: Chain A: D.227, V.228, R.229, A.230, F.241, N.248 Chain B: E.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.230, A:N.248 Water bridges: A:N.246 ACT.21: 7 residues within 4Å: Chain A: E.83 Chain B: D.227, V.228, R.229, A.230, F.241, N.248 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.230, B:N.248 Water bridges: B:N.246

2 x SER: SERINE(Non-functional Binders)

SER.11: 2 residues within 4Å: Ligands: A2G.5, SO4.9 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: S.11, S.11 SER.22: 2 residues within 4Å: Ligands: A2G.16, SO4.20 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: S.22, S.22

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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