SMTL ID : 3ca3.5 (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-tetramer

Ligands

8 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) NAG-FUC-NAG.33: 2 residues within 4Å: Chain C: N.63, D.114 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.34: 5 residues within 4Å: Chain C: G.53, K.54, N.71, T.74 Ligands: SO4.41 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.49: 2 residues within 4Å: Chain D: N.63, D.114 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.50: 5 residues within 4Å: Chain D: G.53, K.54, N.71, T.74 Ligands: SO4.57 No protein-ligand interaction detected (PLIP)

4 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 NAG-NAG.35: 6 residues within 4Å: Chain C: V.133, Q.166, N.178, R.181, L.256, P.257 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.181 NAG-NAG.51: 6 residues within 4Å: Chain D: V.133, Q.166, N.178, R.181, L.256, P.257 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.181

4 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 NAG.36: 3 residues within 4Å: Chain C: N.232, S.234, L.235 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.232 NAG.52: 3 residues within 4Å: Chain D: N.232, S.234, L.235 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.232

8 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: 13 residues within 4Å: Chain A: K.193, D.227, R.229, A.230, S.231, I.239, F.241, N.246, N.248 Chain C: D.47, E.83, P.93 Ligands: NGA.8 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:A.230, A:N.248, C:E.83 Water bridges: A:K.193, A:R.229, A:N.246, C:E.83 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 9 PLIP interactions: 9 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:N.38 Water bridges: B:Q.29, B:Q.36 A2G.22: 13 residues within 4Å: Chain B: K.193, D.227, R.229, A.230, S.231, I.239, F.241, N.246, N.248 Chain D: D.47, E.83, P.93 Ligands: NGA.24 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:A.230, B:N.248, D:E.83 Water bridges: B:K.193, B:R.229, B:N.246, D:D.47 A2G.37: 11 residues within 4Å: Chain C: D.16, V.17, R.18, N.19, G.20, Q.29, W.31, Q.36, N.38, R.107 Ligands: NGA.39 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Q.36 Hydrogen bonds: C:D.16, C:N.19, C:N.19, C:G.20, C:Q.29, C:Q.36, C:N.38 Water bridges: C:Q.29, C:Q.36 A2G.38: 13 residues within 4Å: Chain A: D.47, E.83, P.93 Chain C: K.193, D.227, R.229, A.230, S.231, I.239, F.241, N.246, N.248 Ligands: NGA.40 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:D.227, C:A.230, C:N.248, C:N.248, A:E.83 Water bridges: C:K.193, C:K.193, C:R.229, C:N.246, A:E.83 A2G.53: 11 residues within 4Å: Chain D: D.16, V.17, R.18, N.19, G.20, Q.29, W.31, Q.36, N.38, R.107 Ligands: NGA.55 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Q.36 Hydrogen bonds: D:D.16, D:N.19, D:N.19, D:G.20, D:Q.29, D:N.38 Water bridges: D:Q.29, D:Q.36 A2G.54: 13 residues within 4Å: Chain B: D.47, E.83, P.93 Chain D: K.193, D.227, R.229, A.230, S.231, I.239, F.241, N.246, N.248 Ligands: NGA.56 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:A.230, D:N.248, B:E.83 Water bridges: D:K.193, D:R.229, D:N.246, B:D.47

8 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: 11 residues within 4Å: Chain A: D.227, R.229, A.230, S.231, F.241, N.246, N.248 Chain C: D.47, E.83, P.93 Ligands: A2G.6 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:A.230, A:N.248, A:Q.249, C:D.47, C:E.83, C:E.83 Water bridges: A:K.193, A:R.229, 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 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.29, B:Q.36, B:N.38 Water bridges: B:R.107 NGA.24: 11 residues within 4Å: Chain B: D.227, R.229, A.230, S.231, F.241, N.246, N.248 Chain D: D.47, E.83, P.93 Ligands: A2G.22 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:A.230, B:N.248, B:Q.249, D:D.47, D:E.83 Water bridges: B:K.193, B:R.229, B:N.246, D:D.47, D:D.47 NGA.39: 10 residues within 4Å: Chain C: D.16, V.17, N.19, G.20, Q.29, W.31, Q.36, N.38, R.107 Ligands: A2G.37 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Q.36 Hydrogen bonds: C:D.16, C:N.19, C:N.19, C:G.20, C:Q.29, C:Q.29, C:Q.36, C:Q.36, C:N.38 Water bridges: C:R.107 NGA.40: 11 residues within 4Å: Chain A: D.47, E.83, P.93 Chain C: D.227, R.229, A.230, S.231, F.241, N.246, N.248 Ligands: A2G.38 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:D.227, C:A.230, C:N.248, C:Q.249, A:D.47, A:E.83, A:E.83, A:E.83 Water bridges: C:K.193, C:K.193, C:R.229, C:R.229, C:N.246 NGA.55: 10 residues within 4Å: Chain D: D.16, V.17, N.19, G.20, Q.29, W.31, Q.36, N.38, R.107 Ligands: A2G.53 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Q.36 Hydrogen bonds: D:D.16, D:N.19, D:N.19, D:G.20, D:Q.29, D:Q.29, D:Q.36, D:N.38 Water bridges: D:R.107 NGA.56: 11 residues within 4Å: Chain B: D.47, E.83, P.93 Chain D: D.227, R.229, A.230, S.231, F.241, N.246, N.248 Ligands: A2G.54 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:A.230, D:N.248, D:Q.249, B:D.47, B:E.83 Water bridges: D:K.193, D:R.229, D:N.246, B:D.47, B:D.47

28 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 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: R.18, N.19, R.107 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: S.162, L.163, Q.164 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain A: T.4, R.37, R.40 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: A.75, A.76, E.77 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: R.37, M.52, G.53 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain A: K.193, R.229 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain B: N.71, C.72, S.73 Ligands: NAG-FUC-NAG.18 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain B: R.18, N.19, R.107 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: S.162, L.163, Q.164 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain B: T.4, R.37, R.40 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain B: A.75, A.76, E.77 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain B: R.37, M.52, G.53 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain B: K.193, R.229 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain C: N.71, C.72, S.73 Ligands: NAG-FUC-NAG.34 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain C: R.18, N.19, R.107 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain C: S.162, L.163, Q.164 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain C: T.4, R.37, R.40 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain C: A.75, A.76, E.77 Ligand excluded by PLIP SO4.46: 3 residues within 4Å: Chain C: R.37, M.52, G.53 Ligand excluded by PLIP SO4.47: 2 residues within 4Å: Chain C: K.193, R.229 Ligand excluded by PLIP SO4.57: 4 residues within 4Å: Chain D: N.71, C.72, S.73 Ligands: NAG-FUC-NAG.50 Ligand excluded by PLIP SO4.58: 3 residues within 4Å: Chain D: R.18, N.19, R.107 Ligand excluded by PLIP SO4.59: 3 residues within 4Å: Chain D: S.162, L.163, Q.164 Ligand excluded by PLIP SO4.60: 3 residues within 4Å: Chain D: T.4, R.37, R.40 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain D: A.75, A.76, E.77 Ligand excluded by PLIP SO4.62: 3 residues within 4Å: Chain D: R.37, M.52, G.53 Ligand excluded by PLIP SO4.63: 2 residues within 4Å: Chain D: K.193, R.229 Ligand excluded by PLIP

4 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 ACT.48: 4 residues within 4Å: Chain C: G.25, N.59, V.68, F.70 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:N.59, C:V.68, C:F.70 Water bridges: C:G.60, C:G.60 ACT.64: 4 residues within 4Å: Chain D: G.25, N.59, V.68, F.70 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:N.59, D:V.68, D:F.70 Water bridges: D:G.60, D: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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Agglutinin II

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