SMTL ID : 4u36.1

Crystal structure of a seed lectin from Vatairea macrocarpa complexed with Tn-antigen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.1: 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.1, H2O.1 MN.10: 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.10, H2O.10 MN.19: 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.19, H2O.19 MN.28: 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.28, H2O.28

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 4 residues within 4Å: Chain A: D.125, F.127, N.129, D.132 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.125, A:F.127, A:D.132, H2O.1, H2O.3 CA.11: 4 residues within 4Å: Chain B: D.125, F.127, N.129, D.132 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:F.127, B:D.132, H2O.10, H2O.12 CA.20: 4 residues within 4Å: Chain C: D.125, F.127, N.129, D.132 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.125, C:F.127, C:D.132, H2O.19, H2O.21 CA.29: 4 residues within 4Å: Chain D: D.125, F.127, N.129, D.132 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.125, D:F.127, D:D.132, H2O.28, H2O.30

16 x SO4: SULFATE ION(Non-covalent)(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: N.129, T.130 Ligands: SER.8, A2G.9 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: K.84, F.127, H.217 Ligands: CIT.7 Ligand excluded by PLIP SO4.5: 1 residues within 4Å: Chain A: R.215 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: K.38, R.215 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain B: N.129, T.130 Ligands: SER.17, A2G.18 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain B: K.84, F.127, H.217 Ligands: CIT.16 Ligand excluded by PLIP SO4.14: 1 residues within 4Å: Chain B: R.215 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain B: K.38, R.215 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain C: N.129, T.130 Ligands: SER.26, A2G.27 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain C: K.84, F.127, H.217 Ligands: CIT.25 Ligand excluded by PLIP SO4.23: 1 residues within 4Å: Chain C: R.215 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain C: K.38, R.215 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain D: N.129, T.130 Ligands: SER.35, A2G.36 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain D: K.84, F.127, H.217 Ligands: CIT.34 Ligand excluded by PLIP SO4.32: 1 residues within 4Å: Chain D: R.215 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain D: K.38, R.215 Ligand excluded by PLIP

4 x CIT: CITRIC ACID(Non-functional Binders)(Non-covalent)

CIT.7: 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: SO4.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.136 Hydrogen bonds: A:T.85, A:T.85, A:T.126, A:T.126, A:R.136 Water bridges: A:R.136, A:R.136 Salt bridges: A:K.84, A:R.136, A:H.217 CIT.16: 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: SO4.13 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.136 Hydrogen bonds: B:T.85, B:T.85, B:T.126, B:T.126, B:R.136 Water bridges: B:R.136, B:R.136 Salt bridges: B:K.84, B:R.136, B:H.217 CIT.25: 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: SO4.22 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:R.136 Hydrogen bonds: C:T.85, C:T.85, C:T.126, C:T.126, C:R.136 Water bridges: C:R.136, C:R.136 Salt bridges: C:K.84, C:R.136, C:H.217 CIT.34: 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: SO4.31 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:T.126, D:R.136 Water bridges: D:R.136, D:R.136 Salt bridges: D:K.84, D:R.136, D:H.217

4 x SER: SERINE(Non-functional Binders)(Non-covalent)

SER.8: 2 residues within 4Å: Ligands: SO4.3, A2G.9 4 PLIP interactions: 4 Ligand-Ligand interactions Hydrogen bonds: S.8, S.8, S.8, S.8 SER.17: 2 residues within 4Å: Ligands: SO4.12, A2G.18 4 PLIP interactions: 4 Ligand-Ligand interactions Hydrogen bonds: S.17, S.17, S.17, S.17 SER.26: 2 residues within 4Å: Ligands: SO4.21, A2G.27 4 PLIP interactions: 4 Ligand-Ligand interactions Hydrogen bonds: S.26, S.26, S.26, S.26 SER.35: 2 residues within 4Å: Ligands: SO4.30, A2G.36 4 PLIP interactions: 4 Ligand-Ligand interactions Hydrogen bonds: S.35, S.35, S.35, S.35

4 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.9: 12 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 Ligands: SO4.3, SER.8 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:D.87, A:G.105, A:N.129, A:N.129, A:L.213, A:S.214 Water bridges: S.8, S.8 A2G.18: 12 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 Ligands: SO4.12, SER.17 8 PLIP interactions: 6 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:D.87, B:G.105, B:N.129, B:N.129, B:L.213, B:S.214 Water bridges: S.17, S.17 A2G.27: 12 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 Ligands: SO4.21, SER.26 8 PLIP interactions: 6 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:D.87, C:G.105, C:N.129, C:N.129, C:L.213, C:S.214 Water bridges: S.26, S.26 A2G.36: 12 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 Ligands: SO4.30, SER.35 8 PLIP interactions: 6 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:D.87, D:G.105, D:N.129, D:N.129, D:L.213, D:S.214 Water bridges: S.35, S.35

Links

RCSB   PDBe   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
A

B
A

C
A

D
A

Seed lectin

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