SMTL ID : 2zbj.1

Crystal structure of Dioclea rostrata lectin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: Y.12, N.14, G.98, D.208, G.227, R.228 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.14, A:D.208, A:R.228 Salt bridges: A:R.228 PO4.4: 6 residues within 4Å: Chain B: Y.12, N.14, G.98, D.208, G.227, R.228 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.14, B:D.208, B:R.228 Salt bridges: B:R.228 PO4.7: 6 residues within 4Å: Chain C: Y.12, N.14, G.98, D.208, G.227, R.228 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.14, C:D.208, C:R.228 Salt bridges: C:R.228 PO4.10: 6 residues within 4Å: Chain D: Y.12, N.14, G.98, D.208, G.227, R.228 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.14, D:D.208, D:R.228 Salt bridges: D:R.228

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

MN.2: 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.85, H2O.86 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.187, H2O.188 MN.8: 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.289, H2O.290 MN.11: 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.391, H2O.392

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.67, H2O.74 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.169, H2O.176 CA.9: 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.271, H2O.278 CA.12: 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.373, H2O.380

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

de Oliveira, T.M. et al., Crystal structure of Dioclea rostrata lectin: Insights into understanding the pH-dependent dimer-tetramer equilibrium and the structural basis for carbohydrate recognition in Diocleinae lectins. J.Struct.Biol. (2008)

Release Date

2008-08-19

Peptides

Lectin alpha chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Lectin alpha chain