- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.74 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x CA: CALCIUM ION(Non-covalent)
- 4 x MN: MANGANESE (II) ION(Non-covalent)
MN.2: 4 residues within 4Å:- Chain A: E.123, D.125, D.132, H.137
6 PLIP interactions:4 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:E.123, A:D.125, A:D.132, A:H.137, H2O.3, H2O.6
MN.11: 4 residues within 4Å:- Chain B: E.123, D.125, D.132, H.137
6 PLIP interactions:4 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:E.123, B:D.125, B:D.132, B:H.137, H2O.8, H2O.11
MN.20: 4 residues within 4Å:- Chain C: E.123, D.125, D.132, H.137
6 PLIP interactions:4 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:E.123, C:D.125, C:D.132, C:H.137, H2O.13, H2O.17
MN.29: 4 residues within 4Å:- Chain D: E.123, D.125, D.132, H.137
6 PLIP interactions:4 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:E.123, D:D.125, D:D.132, D:H.137, H2O.19, H2O.22
- 4 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)
A2G.3: 10 residues within 4Å:- Chain A: A.86, D.87, G.104, G.105, F.127, N.129, G.212, L.213, S.214, H.217
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:D.87, A:G.105, A:N.129, A:N.129, A:L.213, A:S.214, A:H.217
A2G.12: 10 residues within 4Å:- Chain B: A.86, D.87, G.104, G.105, F.127, N.129, G.212, L.213, S.214, H.217
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:D.87, B:G.105, B:N.129, B:N.129, B:L.213, B:S.214, B:H.217
A2G.21: 10 residues within 4Å:- Chain C: A.86, D.87, G.104, G.105, F.127, N.129, G.212, L.213, S.214, H.217
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:D.87, C:G.105, C:N.129, C:N.129, C:L.213, C:S.214, C:S.214
A2G.30: 10 residues within 4Å:- Chain D: A.86, D.87, G.104, G.105, F.127, N.129, G.212, L.213, S.214, H.217
7 PLIP interactions:7 interactions with chain D- Hydrogen bonds: D:D.87, D:G.105, D:N.129, D:N.129, D:L.213, D:S.214, D:S.214
- 4 x CIT: CITRIC ACID(Non-functional Binders)
CIT.4: 11 residues within 4Å:- Chain A: S.83, K.84, T.85, T.126, F.127, S.128, S.134, A.135, R.136, H.217
- Ligands: SO4.7
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:R.136
- Hydrogen bonds: A:T.85, A:T.85, A:T.126, A:S.128, A:R.136
- Water bridges: A:S.128, A:R.136
- Salt bridges: A:R.136, A:H.217
CIT.13: 11 residues within 4Å:- Chain B: S.83, K.84, T.85, T.126, F.127, S.128, S.134, A.135, R.136, H.217
- Ligands: SO4.16
10 PLIP interactions:10 interactions with chain B- Hydrophobic interactions: B:R.136
- Hydrogen bonds: B:T.85, B:T.85, B:T.126, B:S.128, B:R.136
- Water bridges: B:S.128, B:R.136
- Salt bridges: B:R.136, B:H.217
CIT.22: 11 residues within 4Å:- Chain C: S.83, K.84, T.85, T.126, F.127, S.128, S.134, A.135, R.136, H.217
- Ligands: SO4.25
10 PLIP interactions:10 interactions with chain C- Hydrophobic interactions: C:R.136
- Hydrogen bonds: C:T.85, C:T.85, C:T.126, C:S.128, C:R.136
- Water bridges: C:S.128, C:R.136
- Salt bridges: C:R.136, C:H.217
CIT.31: 11 residues within 4Å:- Chain D: S.83, K.84, T.85, T.126, F.127, S.128, S.134, A.135, R.136, H.217
- Ligands: SO4.34
11 PLIP interactions:11 interactions with chain D- Hydrophobic interactions: D:R.136
- Hydrogen bonds: D:T.85, D:T.85, D:T.126, D:S.128, D:R.136
- Water bridges: D:S.128, D:R.136, D:H.137
- Salt bridges: D:R.136, D:H.217
- 8 x GOL: GLYCEROL(Non-functional Binders)
GOL.5: 8 residues within 4Å:- Chain A: Y.164, S.166, T.175
- Chain B: N.162, Y.164, S.177, L.178, T.179
7 PLIP interactions:2 interactions with chain B, 5 interactions with chain A- Hydrogen bonds: B:S.177, B:T.179, A:S.166, A:S.166, A:S.166
- Water bridges: A:T.175, A:T.175
GOL.6: 4 residues within 4Å:- Chain A: S.68, E.168, A.169, S.170
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:S.68, A:S.68, A:E.168, A:E.168, A:A.169, A:S.170, A:S.170
- Water bridges: A:Y.167
GOL.14: 8 residues within 4Å:- Chain A: N.162, Y.164, S.177, L.178, T.179
- Chain B: Y.164, S.166, T.175
7 PLIP interactions:2 interactions with chain A, 5 interactions with chain B- Hydrogen bonds: A:S.177, A:T.179, B:S.166, B:S.166, B:S.166
- Water bridges: B:T.175, B:T.175
GOL.15: 4 residues within 4Å:- Chain B: S.68, E.168, A.169, S.170
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:S.68, B:S.68, B:E.168, B:E.168, B:A.169, B:S.170, B:S.170
- Water bridges: B:Y.167
GOL.23: 8 residues within 4Å:- Chain C: Y.164, S.166, T.175
- Chain D: N.162, Y.164, S.177, L.178, T.179
6 PLIP interactions:5 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:S.166, C:S.166, C:S.166, D:S.177
- Water bridges: C:T.175, C:T.175
GOL.24: 4 residues within 4Å:- Chain C: S.68, E.168, A.169, S.170
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:S.68, C:S.68, C:E.168, C:A.169, C:S.170, C:S.170
- Water bridges: C:Y.167
GOL.32: 8 residues within 4Å:- Chain C: N.162, Y.164, S.177, L.178, T.179
- Chain D: Y.164, S.166, T.175
6 PLIP interactions:1 interactions with chain C, 5 interactions with chain D- Hydrogen bonds: C:S.177, D:S.166, D:S.166, D:S.166
- Water bridges: D:T.175, D:T.175
GOL.33: 4 residues within 4Å:- Chain D: S.68, E.168, A.169, S.170
7 PLIP interactions:7 interactions with chain D- Hydrogen bonds: D:S.68, D:S.68, D:E.168, D:A.169, D:S.170, D:S.170
- Water bridges: D:Y.167
- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.7: 4 residues within 4Å:- Chain A: K.84, F.127, H.217
- Ligands: CIT.4
2 PLIP interactions:2 interactions with chain A- Salt bridges: A:K.84, A:H.217
SO4.8: 1 residues within 4Å:- Chain A: R.215
2 PLIP interactions:2 interactions with chain A- Water bridges: A:R.215
- Salt bridges: A:R.215
SO4.9: 3 residues within 4Å:- Chain A: T.27, K.29, K.31
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:T.27
- Water bridges: A:K.29
- Salt bridges: A:K.29, A:K.31
SO4.16: 4 residues within 4Å:- Chain B: K.84, F.127, H.217
- Ligands: CIT.13
2 PLIP interactions:2 interactions with chain B- Salt bridges: B:K.84, B:H.217
SO4.17: 1 residues within 4Å:- Chain B: R.215
2 PLIP interactions:2 interactions with chain B- Water bridges: B:R.215
- Salt bridges: B:R.215
SO4.18: 3 residues within 4Å:- Chain B: T.27, K.29, K.31
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:T.27
- Water bridges: B:K.29
- Salt bridges: B:K.29, B:K.31
SO4.25: 4 residues within 4Å:- Chain C: K.84, F.127, H.217
- Ligands: CIT.22
2 PLIP interactions:2 interactions with chain C- Salt bridges: C:K.84, C:H.217
SO4.26: 1 residues within 4Å:- Chain C: R.215
2 PLIP interactions:2 interactions with chain C- Water bridges: C:R.215
- Salt bridges: C:R.215
SO4.27: 3 residues within 4Å:- Chain C: T.27, K.29, K.31
3 PLIP interactions:3 interactions with chain C- Water bridges: C:K.29
- Salt bridges: C:K.29, C:K.31
SO4.34: 4 residues within 4Å:- Chain D: K.84, F.127, H.217
- Ligands: CIT.31
2 PLIP interactions:2 interactions with chain D- Salt bridges: D:K.84, D:H.217
SO4.35: 1 residues within 4Å:- Chain D: R.215
2 PLIP interactions:2 interactions with chain D- Water bridges: D:R.215
- Salt bridges: D:R.215
SO4.36: 3 residues within 4Å:- Chain D: T.27, K.29, K.31
3 PLIP interactions:3 interactions with chain D- Water bridges: D:K.29
- Salt bridges: D:K.29, D:K.31
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Sousa, B.L. et al., High-resolution structure of a new Tn antigen-binding lectin from Vatairea macrocarpa and a comparative analysis of Tn-binding legume lectins. Int.J.Biochem.Cell Biol. (2014)
- Release Date
- 2014-12-31
- Peptides
- Seed lectin: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.74 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x CA: CALCIUM ION(Non-covalent)
- 4 x MN: MANGANESE (II) ION(Non-covalent)
- 4 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)
- 4 x CIT: CITRIC ACID(Non-functional Binders)
- 8 x GOL: GLYCEROL(Non-functional Binders)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Sousa, B.L. et al., High-resolution structure of a new Tn antigen-binding lectin from Vatairea macrocarpa and a comparative analysis of Tn-binding legume lectins. Int.J.Biochem.Cell Biol. (2014)
- Release Date
- 2014-12-31
- Peptides
- Seed lectin: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A