- Coordinates
- PDB Format
- 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
- 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.15: 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.27: 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.39: 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.16: 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.28: 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.40: 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 AMG: methyl alpha-D-galactopyranoside(Non-covalent)
AMG.5: 10 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
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:D.16, A:N.19, A:G.20, A:Q.29, A:Q.29, A:Q.36, A:N.38
- Water bridges: A:R.107
AMG.6: 10 residues within 4Å:- Chain A: D.227, V.228, R.229, A.230, I.239, F.241, N.248
- Chain C: D.47, E.83, P.93
12 PLIP interactions:4 interactions with chain C, 8 interactions with chain A- Hydrogen bonds: C:E.83, A:D.227, A:A.230, A:N.248, A:N.248
- Water bridges: C:D.47, C:E.83, C:P.93, A:K.193, A:R.229, A:R.229, A:N.246
AMG.17: 10 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
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:D.16, B:N.19, B:G.20, B:Q.29, B:Q.29, B:Q.36, B:N.38
- Water bridges: B:R.107
AMG.18: 10 residues within 4Å:- Chain B: D.227, V.228, R.229, A.230, I.239, F.241, N.248
- Chain D: D.47, E.83, P.93
11 PLIP interactions:8 interactions with chain B, 3 interactions with chain D- Hydrogen bonds: B:D.227, B:A.230, B:N.248, B:N.248
- Water bridges: B:K.193, B:R.229, B:R.229, B:N.246, D:D.47, D:E.83, D:P.93
AMG.29: 10 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
8 PLIP interactions:8 interactions with chain C- Hydrogen bonds: C:D.16, C:N.19, C:G.20, C:Q.29, C:Q.29, C:Q.36, C:N.38
- Water bridges: C:R.107
AMG.30: 10 residues within 4Å:- Chain A: D.47, E.83, P.93
- Chain C: D.227, V.228, R.229, A.230, I.239, F.241, N.248
12 PLIP interactions:8 interactions with chain C, 4 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:R.229, C:R.229, C:N.246, A:D.47, A:E.83, A:P.93
AMG.41: 10 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
8 PLIP interactions:8 interactions with chain D- Hydrogen bonds: D:D.16, D:N.19, D:G.20, D:Q.29, D:Q.29, D:Q.36, D:N.38
- Water bridges: D:R.107
AMG.42: 10 residues within 4Å:- Chain B: D.47, E.83, P.93
- Chain D: D.227, V.228, R.229, A.230, I.239, F.241, N.248
11 PLIP interactions:3 interactions with chain B, 8 interactions with chain D- Water bridges: B:D.47, B:E.83, B:P.93, D:K.193, D:R.229, D:R.229, D:N.246
- Hydrogen bonds: D:D.227, D:A.230, D:N.248, D:N.248
- 20 x SO4: SULFATE ION(Non-functional Binders)
SO4.7: 2 residues within 4Å:- Chain A: A.76, E.77
Ligand excluded by PLIPSO4.8: 3 residues within 4Å:- Chain A: T.4, R.37, R.40
Ligand excluded by PLIPSO4.9: 5 residues within 4Å:- Chain A: N.71, C.72, S.73
- Ligands: NAG-FUC-NAG.2, NAG-FUC-NAG.2
Ligand excluded by PLIPSO4.10: 3 residues within 4Å:- Chain A: S.162, L.163, Q.164
Ligand excluded by PLIPSO4.11: 3 residues within 4Å:- Chain A: R.18, N.19, R.107
Ligand excluded by PLIPSO4.19: 2 residues within 4Å:- Chain B: A.76, E.77
Ligand excluded by PLIPSO4.20: 3 residues within 4Å:- Chain B: T.4, R.37, R.40
Ligand excluded by PLIPSO4.21: 5 residues within 4Å:- Chain B: N.71, C.72, S.73
- Ligands: NAG-FUC-NAG.14, NAG-FUC-NAG.14
Ligand excluded by PLIPSO4.22: 3 residues within 4Å:- Chain B: S.162, L.163, Q.164
Ligand excluded by PLIPSO4.23: 3 residues within 4Å:- Chain B: R.18, N.19, R.107
Ligand excluded by PLIPSO4.31: 2 residues within 4Å:- Chain C: A.76, E.77
Ligand excluded by PLIPSO4.32: 3 residues within 4Å:- Chain C: T.4, R.37, R.40
Ligand excluded by PLIPSO4.33: 5 residues within 4Å:- Chain C: N.71, C.72, S.73
- Ligands: NAG-FUC-NAG.26, NAG-FUC-NAG.26
Ligand excluded by PLIPSO4.34: 3 residues within 4Å:- Chain C: S.162, L.163, Q.164
Ligand excluded by PLIPSO4.35: 3 residues within 4Å:- Chain C: R.18, N.19, R.107
Ligand excluded by PLIPSO4.43: 2 residues within 4Å:- Chain D: A.76, E.77
Ligand excluded by PLIPSO4.44: 3 residues within 4Å:- Chain D: T.4, R.37, R.40
Ligand excluded by PLIPSO4.45: 5 residues within 4Å:- Chain D: N.71, C.72, S.73
- Ligands: NAG-FUC-NAG.38, NAG-FUC-NAG.38
Ligand excluded by PLIPSO4.46: 3 residues within 4Å:- Chain D: S.162, L.163, Q.164
Ligand excluded by PLIPSO4.47: 3 residues within 4Å:- Chain D: R.18, N.19, R.107
Ligand excluded by PLIP- 4 x ACT: ACETATE ION(Non-functional Binders)
ACT.12: 1 residues within 4Å:- Chain A: N.59
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.59
ACT.24: 1 residues within 4Å:- Chain B: N.59
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:N.59
ACT.36: 1 residues within 4Å:- Chain C: N.59
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:N.59
ACT.48: 1 residues within 4Å:- Chain D: N.59
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D: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: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A
- Coordinates
- PDB Format
- 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
- 4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 8 x AMG: methyl alpha-D-galactopyranoside(Non-covalent)
- 20 x SO4: SULFATE ION(Non-functional Binders)
- 4 x ACT: ACETATE ION(Non-functional Binders)
- 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: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A