SMTL ID : 4xxa.1

Crystal structure of a recombinant Vatairea macrocarpa seed lectin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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.2, H2O.2 CA.5: 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.4, H2O.5 CA.9: 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.7, H2O.8 CA.13: 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.10, H2O.11

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

MN.2: 4 residues within 4Å: Chain A: E.125, D.127, D.134, H.139 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.125, A:D.127, A:D.134, A:H.139, H2O.2, H2O.3 MN.6: 4 residues within 4Å: Chain B: E.125, D.127, D.134, H.139 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.125, B:D.127, B:D.134, B:H.139, H2O.4, H2O.6 MN.10: 4 residues within 4Å: Chain C: E.125, D.127, D.134, H.139 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.125, C:D.127, C:D.134, C:H.139, H2O.8, H2O.9 MN.14: 4 residues within 4Å: Chain D: E.125, D.127, D.134, H.139 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.125, D:D.127, D:D.134, D:H.139, H2O.10, H2O.12

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: A.88, D.89, G.107, F.129, N.131, G.214, L.215, S.216 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.107, A:N.131, A:N.131, A:L.215, A:S.216, A:S.216 GOL.7: 8 residues within 4Å: Chain B: A.88, D.89, G.106, G.107, F.129, N.131, G.214, L.215 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.89, B:G.107, B:N.131, B:L.215 GOL.11: 8 residues within 4Å: Chain C: A.88, D.89, G.107, F.129, N.131, G.214, L.215, S.216 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.107, C:N.131, C:N.131, C:L.215, C:S.216, C:S.216 GOL.15: 8 residues within 4Å: Chain D: A.88, D.89, G.106, G.107, F.129, N.131, G.214, L.215 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.89, D:G.107, D:N.131, D:L.215

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 4 residues within 4Å: Chain A: H.47, K.104, D.105, L.215 No protein-ligand interaction detected (PLIP) 1PE.8: 3 residues within 4Å: Chain B: E.80, N.159, G.160 No protein-ligand interaction detected (PLIP) 1PE.12: 4 residues within 4Å: Chain C: H.47, K.104, D.105, L.215 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.105 1PE.16: 3 residues within 4Å: Chain D: E.80, N.159, G.160 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.80

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
B

C
A

D
B

Seed lectin

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