SMTL ID : 4wv8.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-tetramer

Ligands

4 x GLC- GAL: beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GAL.1: 10 residues within 4Å: Chain A: A.87, D.88, G.105, G.106, F.128, N.130, G.213, L.214, S.215, H.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.88, A:G.106, A:N.130, A:N.130, A:L.214, A:S.215, A:H.218, A:S.215 Water bridges: A:S.215, A:S.215, A:S.215 GLC-GAL.2: 10 residues within 4Å: Chain B: A.87, D.88, G.105, G.106, F.128, N.130, G.213, L.214, S.215, H.218 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.88, B:G.106, B:N.130, B:N.130, B:L.214, B:H.218, B:S.215 Water bridges: B:S.215, B:S.215 GLC-GAL.3: 10 residues within 4Å: Chain C: A.87, D.88, G.105, G.106, F.128, N.130, G.213, L.214, S.215, H.218 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.88, C:G.106, C:N.130, C:N.130, C:L.214, C:H.218, C:S.215 GLC-GAL.4: 10 residues within 4Å: Chain D: A.87, D.88, G.105, G.106, F.128, N.130, G.213, L.214, S.215, H.218 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.88, D:G.106, D:N.130, D:N.130, D:L.214, D:S.215, D:S.215

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.126, F.128, N.130, D.133 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.126, A:D.126, A:F.128, H2O.3, H2O.3 CA.7: 4 residues within 4Å: Chain B: D.126, F.128, N.130, D.133 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.126, B:D.126, B:F.128, B:D.133, H2O.11 CA.9: 4 residues within 4Å: Chain C: D.126, F.128, N.130, D.133 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.126, C:D.126, C:F.128, H2O.17, H2O.18 CA.11: 4 residues within 4Å: Chain D: D.126, F.128, N.130, D.133 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.126, D:F.128, D:D.133, H2O.22, H2O.25

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

MN.6: 4 residues within 4Å: Chain A: E.124, D.126, D.133, H.138 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.124, A:D.126, A:D.133, A:H.138, H2O.2, H2O.3 MN.8: 4 residues within 4Å: Chain B: E.124, D.126, D.133, H.138 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.124, B:D.126, B:D.133, B:H.138, H2O.11, H2O.11 MN.10: 4 residues within 4Å: Chain C: E.124, D.126, D.133, H.138 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.124, C:D.126, C:D.133, C:H.138, H2O.16, H2O.16 MN.12: 4 residues within 4Å: Chain D: E.124, D.126, D.133, H.138 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.124, D:D.126, D:D.133, D:H.138, H2O.22, H2O.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sousa, B.L. et al., Structural characterization of a Vatairea macrocarpa lectin in complex with a tumor-associated antigen: A new tool for cancer research. 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
C

D
D

Seed lectin