SMTL ID : 3ca3.3 (4 other biounits)

Crystal structure of Sambucus Nigra Agglutinin II (SNA-II)-tetragonal crystal form- complexed to N-Acetylgalactosamine

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: 2 residues within 4Å: Chain A: N.63, D.114 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.2: 5 residues within 4Å: Chain A: G.53, K.54, N.71, T.74 Ligands: SO4.9 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.17: 2 residues within 4Å: Chain B: N.63, D.114 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.18: 5 residues within 4Å: Chain B: G.53, K.54, N.71, T.74 Ligands: SO4.25 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.19: 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.20: 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 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: NGA.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Q.36 Hydrogen bonds: A:D.16, A:N.19, A:N.19, A:G.20, A:Q.29, A:N.38 Water bridges: A:Q.29, A:Q.36 A2G.6: 10 residues within 4Å: Chain A: K.193, D.227, R.229, A.230, S.231, I.239, F.241, N.246, N.248 Ligands: NGA.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.230, A:N.248 Water bridges: A:K.193, A:R.229, A:N.246, A:N.248 A2G.21: 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: NGA.23 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Q.36 Hydrogen bonds: B:D.16, B:N.19, B:N.19, B:G.20, B:Q.29, B:Q.36, B:N.38 Water bridges: B:Q.29, B:Q.36 A2G.22: 10 residues within 4Å: Chain B: K.193, D.227, R.229, A.230, S.231, I.239, F.241, N.246, N.248 Ligands: NGA.24 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.230, B:N.248 Water bridges: B:K.193, B:R.229, B:N.246, B:N.248

4 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA.7: 10 residues within 4Å: Chain A: D.16, V.17, N.19, G.20, Q.29, W.31, Q.36, N.38, R.107 Ligands: A2G.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Q.36 Hydrogen bonds: A:D.16, A:N.19, A:N.19, A:G.20, A:Q.29, A:Q.29, A:Q.36, A:N.38 Water bridges: A:R.107 NGA.8: 8 residues within 4Å: Chain A: D.227, R.229, A.230, S.231, F.241, N.246, N.248 Ligands: A2G.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.230, A:N.248, A:Q.249 Water bridges: A:K.193, A:R.229, A:A.230, A:N.246 NGA.23: 10 residues within 4Å: Chain B: D.16, V.17, N.19, G.20, Q.29, W.31, Q.36, N.38, R.107 Ligands: A2G.21 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Q.36 Hydrogen bonds: B:D.16, B:N.19, B:N.19, B:G.20, B:Q.29, B:Q.29, B:Q.36, B:Q.36, B:N.38 Water bridges: B:R.107 NGA.24: 8 residues within 4Å: Chain B: D.227, R.229, A.230, S.231, F.241, N.246, N.248 Ligands: A2G.22 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.230, B:N.248, B:Q.249 Water bridges: B:K.193, B:R.229, B:A.230, B:N.246

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

SO4.9: 4 residues within 4Å: Chain A: N.71, C.72, S.73 Ligands: 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: 3 residues within 4Å: Chain A: R.18, N.19, R.107 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.19 Water bridges: A:R.107, A:R.107 Salt bridges: A:R.18, A:R.107 SO4.11: 7 residues within 4Å: Chain A: S.162, L.163, Q.164 Chain B: S.162, L.163, Q.164 Ligands: SO4.27 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.162, A:L.163, A:Q.164, B:L.163, B:Q.164 Water bridges: A:Q.145, A:Q.145, B:Q.145, B:Q.145, B:T.161 SO4.12: 3 residues within 4Å: Chain A: T.4, R.37, R.40 9 PLIP interactions: 9 interactions with chain A Water bridges: A:T.4, A:T.4, A:T.4, A:T.4, A:R.5, A:R.37, A:R.40 Salt bridges: A:R.37, A:R.40 SO4.13: 3 residues within 4Å: Chain A: A.75, A.76, E.77 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.75, A:E.77 Water bridges: A:N.78 SO4.14: 3 residues within 4Å: Chain A: R.37, M.52, G.53 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.52, A:G.53 Water bridges: A:T.4, A:R.37, A:R.37 Salt bridges: A:R.37 SO4.15: 2 residues within 4Å: Chain A: K.193, R.229 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.229, A:R.229 Salt bridges: A:K.193, A:R.229 SO4.25: 4 residues within 4Å: Chain B: N.71, C.72, S.73 Ligands: NAG-FUC-NAG.18 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 SO4.26: 3 residues within 4Å: Chain B: R.18, N.19, R.107 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.19 Water bridges: B:R.107, B:R.107 Salt bridges: B:R.18, B:R.107 SO4.27: 7 residues within 4Å: Chain A: S.162, L.163, Q.164 Chain B: S.162, L.163, Q.164 Ligands: SO4.11 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:L.163, A:Q.164, B:S.162, B:L.163, B:Q.164 Water bridges: A:Q.145, A:Q.145, A:T.161, B:Q.145, B:Q.145 SO4.28: 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:R.5, B:R.37, B:R.40 Salt bridges: B:R.37, B:R.40 SO4.29: 3 residues within 4Å: Chain B: A.75, A.76, E.77 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.75, B:E.77 Water bridges: B:N.78 SO4.30: 3 residues within 4Å: Chain B: R.37, M.52, G.53 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:M.52, B:G.53 Water bridges: B:R.37, B:R.37, B:T.42 Salt bridges: B:R.37 SO4.31: 2 residues within 4Å: Chain B: K.193, R.229 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.229, B:R.229 Salt bridges: B:K.193, B:R.229

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

ACT.16: 4 residues within 4Å: Chain A: G.25, N.59, V.68, F.70 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.59, A:V.68, A:F.70 Water bridges: A:G.60, A:G.60 ACT.32: 4 residues within 4Å: Chain B: G.25, N.59, V.68, F.70 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.59, B:V.68, B:F.70 Water bridges: B:G.60, B:G.60

Links

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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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