SMTL ID : 3cah.2 (2 other biounits)

Sambucus nigra aggutinin II. tetragonal crystal form- complexed to fucose

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: 3 residues within 4Å: Chain A: N.63, E.113, D.114 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.2: 6 residues within 4Å: Chain A: G.53, K.54, N.71, S.73, T.74 Ligands: SO4.7 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.15: 3 residues within 4Å: Chain B: N.63, E.113, D.114 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.16: 6 residues within 4Å: Chain B: G.53, K.54, N.71, S.73, T.74 Ligands: SO4.21 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.29: 3 residues within 4Å: Chain C: N.63, E.113, D.114 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.30: 6 residues within 4Å: Chain C: G.53, K.54, N.71, S.73, T.74 Ligands: SO4.35 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.43: 3 residues within 4Å: Chain D: N.63, E.113, D.114 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.44: 6 residues within 4Å: Chain D: G.53, K.54, N.71, S.73, T.74 Ligands: SO4.49 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: 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 NAG-NAG.17: 5 residues within 4Å: Chain B: V.133, Q.166, N.178, R.181, P.257 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.181 NAG-NAG.31: 5 residues within 4Å: Chain C: V.133, Q.166, N.178, R.181, P.257 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.181 NAG-NAG.45: 5 residues within 4Å: Chain D: V.133, Q.166, N.178, R.181, 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.18: 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.32: 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.46: 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

4 x FCA: alpha-D-fucopyranose(Non-covalent)

FCA.5: 9 residues within 4Å: Chain A: D.16, V.17, R.18, N.19, G.20, Q.29, W.31, Q.36, N.38 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.16, A:N.19, A:G.20, A:Q.29, A:Q.36, A:N.38 FCA.19: 9 residues within 4Å: Chain B: D.16, V.17, R.18, N.19, G.20, Q.29, W.31, Q.36, N.38 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.16, B:N.19, B:G.20, B:Q.29, B:Q.36, B:N.38 FCA.33: 9 residues within 4Å: Chain C: D.16, V.17, R.18, N.19, G.20, Q.29, W.31, Q.36, N.38 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.16, C:N.19, C:G.20, C:Q.29, C:Q.36, C:N.38 FCA.47: 9 residues within 4Å: Chain D: D.16, V.17, R.18, N.19, G.20, Q.29, W.31, Q.36, N.38 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.16, D:N.19, D:G.20, D:Q.29, D:Q.36, D:N.38

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

SO4.6: 3 residues within 4Å: Chain A: T.4, R.37, R.40 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: N.71, C.72, S.73 Ligands: NAG-FUC-NAG.2 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: R.18, N.19, R.107 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: S.162, L.163, Q.164 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: R.37, M.52, G.53 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: A.76, E.77 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain B: T.4, R.37, R.40 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain B: N.71, C.72, S.73 Ligands: NAG-FUC-NAG.16 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain B: R.18, N.19, R.107 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain B: S.162, L.163, Q.164 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain B: R.37, M.52, G.53 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain B: A.76, E.77 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain C: T.4, R.37, R.40 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain C: N.71, C.72, S.73 Ligands: NAG-FUC-NAG.30 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain C: R.18, N.19, R.107 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain C: S.162, L.163, Q.164 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain C: R.37, M.52, G.53 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain C: A.76, E.77 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain D: T.4, R.37, R.40 Ligand excluded by PLIP SO4.49: 4 residues within 4Å: Chain D: N.71, C.72, S.73 Ligands: NAG-FUC-NAG.44 Ligand excluded by PLIP SO4.50: 3 residues within 4Å: Chain D: R.18, N.19, R.107 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain D: S.162, L.163, Q.164 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain D: R.37, M.52, G.53 Ligand excluded by PLIP SO4.53: 2 residues within 4Å: Chain D: A.76, E.77 Ligand excluded by PLIP

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

ACT.12: 8 residues within 4Å: Chain A: D.227, V.228, R.229, A.230, F.241, N.248 Chain C: E.83 Ligands: ACT.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.228, A:A.230, A:N.248 ACT.13: 5 residues within 4Å: Chain A: P.93 Chain C: K.193, A.230, I.239 Ligands: ACT.40 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.230 Water bridges: C:R.229, C:R.229 Salt bridges: C:K.193, C:R.229 ACT.14: 1 residues within 4Å: Chain A: N.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.59 ACT.26: 8 residues within 4Å: Chain B: D.227, V.228, R.229, A.230, F.241, N.248 Chain D: E.83 Ligands: ACT.55 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.228, B:A.230, B:N.248 ACT.27: 5 residues within 4Å: Chain B: P.93 Chain D: K.193, A.230, I.239 Ligands: ACT.54 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.230 Water bridges: D:R.229, D:R.229 Salt bridges: D:K.193, D:R.229 ACT.28: 1 residues within 4Å: Chain B: N.59 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.59 ACT.40: 8 residues within 4Å: Chain A: E.83 Chain C: D.227, V.228, R.229, A.230, F.241, N.248 Ligands: ACT.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.228, C:A.230, C:N.248 ACT.41: 5 residues within 4Å: Chain A: K.193, A.230, I.239 Chain C: P.93 Ligands: ACT.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.230 Water bridges: A:R.229, A:R.229 Salt bridges: A:K.193, A:R.229 ACT.42: 1 residues within 4Å: Chain C: N.59 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.59 ACT.54: 8 residues within 4Å: Chain B: E.83 Chain D: D.227, V.228, R.229, A.230, F.241, N.248 Ligands: ACT.27 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.228, D:A.230, D:N.248 ACT.55: 5 residues within 4Å: Chain B: K.193, A.230, I.239 Chain D: P.93 Ligands: ACT.26 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.230 Water bridges: B:R.229, B:R.229 Salt bridges: B:K.193, B:R.229 ACT.56: 1 residues within 4Å: Chain D: N.59 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.59

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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