SMTL ID : 8szo.1

Canavalia villosa lectin in complex with alpha-methyl-mannoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24, H2O.1, H2O.3 MN.5: 4 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24, H2O.5, H2O.6 MN.9: 4 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24, H2O.8, H2O.10 MN.13: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24, H2O.11, H2O.13

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:Y.12, A:D.19, H2O.1, H2O.1 CA.6: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:Y.12, B:D.19, H2O.4, H2O.5 CA.10: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.10, C:Y.12, C:D.19, H2O.8, H2O.8 CA.14: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.10, D:Y.12, D:D.19, H2O.11, H2O.11

4 x MMA: methyl alpha-D-mannopyranoside(Non-covalent)

MMA.3: 9 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, M.228 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.98, A:L.99, A:Y.100, A:Y.100, A:M.228 Water bridges: A:G.227 MMA.7: 9 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, M.228 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.98, B:L.99, B:Y.100, B:Y.100, B:M.228 Water bridges: B:G.227 MMA.11: 9 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, M.228 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100, C:M.228 Water bridges: C:G.227 MMA.15: 9 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, M.228 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100, D:M.228 Water bridges: D:G.227

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: I.17, M.228, L.229, P.234, D.235, A.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.236 GOL.8: 6 residues within 4Å: Chain B: I.17, M.228, L.229, P.234, D.235, A.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.236 GOL.12: 6 residues within 4Å: Chain C: I.17, M.228, L.229, P.234, D.235, A.236 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.236 GOL.16: 6 residues within 4Å: Chain D: I.17, M.228, L.229, P.234, D.235, A.236 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lossio, C.F. et al., Lectin from Canavalia villosa seeds: A glucose/mannose-specific protein and a new tool for inflammation studies. Int J Biol Macromol (2017)

Release Date

2023-09-27

Peptides

Canavalia villosa lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Canavalia villosa lectin