SMTL ID : 4xtm.1

Crystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with GalNAc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.127, F.129, N.131, D.134 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.127, A:F.129, A:D.134, H2O.1, H2O.1 CA.7: 4 residues within 4Å: Chain B: D.127, F.129, N.131, D.134 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.127, B:F.129, B:D.134, H2O.2, H2O.2 CA.13: 4 residues within 4Å: Chain C: D.127, F.129, N.131, D.134 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.127, C:F.129, C:D.134, H2O.3, H2O.3 CA.19: 4 residues within 4Å: Chain D: D.127, F.129, N.131, D.134 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.127, D:F.129, D:D.134, H2O.4, H2O.5

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

MN.2: 4 residues within 4Å: Chain A: E.125, D.127, D.134, H.139 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.125, A:D.127, A:D.134, A:H.139, H2O.1 MN.8: 4 residues within 4Å: Chain B: E.125, D.127, D.134, H.139 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.125, B:D.127, B:D.134, B:H.139, H2O.2 MN.14: 4 residues within 4Å: Chain C: E.125, D.127, D.134, H.139 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.125, C:D.127, C:D.134, C:H.139, H2O.3 MN.20: 4 residues within 4Å: Chain D: E.125, D.127, D.134, H.139 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.125, D:D.127, D:D.134, D:H.139, H2O.4

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

A2G.3: 10 residues within 4Å: Chain A: A.88, D.89, G.106, G.107, F.129, N.131, G.214, L.215, S.216, H.219 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.89, A:G.107, A:N.131, A:N.131, A:L.215, A:S.216 A2G.9: 10 residues within 4Å: Chain B: A.88, D.89, G.106, G.107, F.129, N.131, G.214, L.215, S.216, H.219 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.89, B:G.107, B:N.131, B:N.131, B:L.215, B:S.216 A2G.15: 10 residues within 4Å: Chain C: A.88, D.89, G.106, G.107, F.129, N.131, G.214, L.215, S.216, H.219 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.89, C:G.107, C:N.131, C:N.131, C:L.215, C:S.216 A2G.21: 10 residues within 4Å: Chain D: A.88, D.89, G.106, G.107, F.129, N.131, G.214, L.215, S.216, H.219 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.89, D:G.107, D:N.131, D:N.131, D:L.215, D:S.216

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

CIT.4: 11 residues within 4Å: Chain A: S.85, K.86, T.87, T.128, F.129, S.130, S.136, A.137, R.138, H.219 Ligands: SO4.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.138 Hydrogen bonds: A:T.87, A:T.87, A:S.130 Salt bridges: A:H.219 CIT.10: 11 residues within 4Å: Chain B: S.85, K.86, T.87, T.128, F.129, S.130, S.136, A.137, R.138, H.219 Ligands: SO4.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.138 Hydrogen bonds: B:T.87, B:T.87, B:S.130 Salt bridges: B:H.219 CIT.16: 11 residues within 4Å: Chain C: S.85, K.86, T.87, T.128, F.129, S.130, S.136, A.137, R.138, H.219 Ligands: SO4.18 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:R.138 Hydrogen bonds: C:T.87, C:T.87, C:S.130 Salt bridges: C:H.219 CIT.22: 11 residues within 4Å: Chain D: S.85, K.86, T.87, T.128, F.129, S.130, S.136, A.137, R.138, H.219 Ligands: SO4.24 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:R.138 Hydrogen bonds: D:T.87, D:T.87, D:S.130 Salt bridges: D:H.219

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: P.135, S.136, A.137, Y.152, K.154 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.136, A:A.137, A:Y.152, A:K.154 GOL.11: 5 residues within 4Å: Chain B: P.135, S.136, A.137, Y.152, K.154 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.136, B:A.137, B:Y.152, B:K.154 GOL.17: 5 residues within 4Å: Chain C: P.135, S.136, A.137, Y.152, K.154 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.136, C:A.137, C:K.154 GOL.23: 5 residues within 4Å: Chain D: P.135, S.136, A.137, Y.152, K.154 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.136, D:A.137, D:K.154

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

SO4.6: 4 residues within 4Å: Chain A: K.86, F.129, H.219 Ligands: CIT.4 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.86, A:H.219 SO4.12: 4 residues within 4Å: Chain B: K.86, F.129, H.219 Ligands: CIT.10 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.86, B:H.219 SO4.18: 4 residues within 4Å: Chain C: K.86, F.129, H.219 Ligands: CIT.16 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.86, C:H.219 SO4.24: 4 residues within 4Å: Chain D: K.86, F.129, H.219 Ligands: CIT.22 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.86, D:H.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sousa, B.L. et al., Crystal structure of a recombinant Vatairea macrocarpa seed lectin. Int.J.Biochem.Cell Biol. (2016)

Release Date

2016-01-27

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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