SMTL ID : 3ca0.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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

NAG-NAG-BMA-XYP-MAN-MAN-FUC.1: 5 residues within 4Å: Chain A: N.63, G.64, P.102, R.103, E.113 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.102 Hydrogen bonds: A:R.103, A:R.103

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

NAG-FUC.2: 6 residues within 4Å: Chain A: G.53, K.54, N.71, S.73, T.74 Ligands: SO4.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.71 Water bridges: A:G.53, A:K.54, A:N.71

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 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.181

1 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.4: 3 residues within 4Å: Chain A: N.232, S.234, L.235 No protein-ligand interaction detected (PLIP)

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

SO4.5: 4 residues within 4Å: Chain A: R.18, N.19, Y.21, R.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.107 Water bridges: A:Q.29 Salt bridges: A:R.18 SO4.6: 2 residues within 4Å: Chain A: T.4, R.40 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.40 SO4.7: 3 residues within 4Å: Chain A: T.23, D.24, K.54 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.23, A:D.24 Water bridges: A:K.54, A:K.54 Salt bridges: A:K.54 SO4.8: 5 residues within 4Å: Chain A: N.71, C.72, S.73 Ligands: NAG-FUC.2, NAG-FUC.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:C.72, A:S.73, A:S.73 Water bridges: A:R.50, A:R.50, A:G.53, A:N.71 SO4.9: 4 residues within 4Å: Chain A: T.161, S.162, L.163, Q.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.163, A:Q.164, A:Q.164 SO4.10: 3 residues within 4Å: Chain A: G.34, T.35, Q.36 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.35, A:T.35, A:Q.36, A:Q.36 Water bridges: A:C.33 SO4.11: 2 residues within 4Å: Chain A: K.221, R.223 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.221, A:R.223

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

ACT.12: 2 residues within 4Å: Chain A: Y.21, T.23 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.21 Hydrogen bonds: A:T.23 Water bridges: A:D.22

Links

RCSB   PDBe   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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