SMTL ID : 4u2a.1

Structure of a lectin from the seeds of Vatairea macrocarpa complexed with GalNAc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.125, F.127, N.129, D.132 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.125, A:D.125, A:F.127, A:D.132, H2O.3 CA.10: 4 residues within 4Å: Chain B: D.125, F.127, N.129, D.132 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.125, B:D.125, B:F.127, B:D.132, H2O.8 CA.19: 4 residues within 4Å: Chain C: D.125, F.127, N.129, D.132 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.125, C:D.125, C:F.127, C:D.132, H2O.14 CA.28: 4 residues within 4Å: Chain D: D.125, F.127, N.129, D.132 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.125, D:D.125, D:F.127, D:D.132, H2O.19

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
A

B
A

C
A

D
A

Seed lectin

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