SMTL ID : 3c9z.1

Sambucus nigra agglutinin II (SNA-II), tetragonal crystal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

2 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: 4 residues within 4Å: Chain A: N.63, E.113, D.114, I.116 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.2: 5 residues within 4Å: Chain A: G.53, K.54, N.71, S.73 Ligands: SO4.5 No protein-ligand interaction detected (PLIP)

1 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: 5 residues within 4Å: Chain A: V.133, Q.166, N.178, R.181, P.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.130 Water bridges: A:R.181

1 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 Water bridges: A:N.232

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

SO4.5: 5 residues within 4Å: Chain A: N.71, C.72, S.73 Ligands: NAG-FUC-NAG.2, NAG-FUC-NAG.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.71, A:C.72, A:S.73, A:S.73 SO4.6: 3 residues within 4Å: Chain A: R.18, N.19, R.107 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.19, A:R.107 Water bridges: A:N.19 Salt bridges: A:R.18 SO4.7: 3 residues within 4Å: Chain A: S.162, L.163, Q.164 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.163, A:Q.164, A:Q.164 Water bridges: A:T.161 SO4.8: 3 residues within 4Å: Chain A: T.4, R.37, R.40 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.37 Salt bridges: A:R.37, A:R.40

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

ACT.9: 1 residues within 4Å: Chain A: N.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A: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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Agglutinin II

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