SMTL ID : 2je7.1

Crystal structure of recombinant Dioclea guianensis lectin S131H complexed with 5-bromo-4-chloro-3-indolyl-a-D-mannose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: E.10, D.12, D.21, H.26 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.10, A:D.12, A:D.21, A:H.26, H2O.10, H2O.10 MN.4: 4 residues within 4Å: Chain B: E.10, D.12, D.21, H.26 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.10, B:D.12, B:D.21, B:H.26, H2O.20, H2O.20 MN.7: 4 residues within 4Å: Chain C: E.10, D.12, D.21, H.26 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.10, C:D.12, C:D.21, C:H.26, H2O.30, H2O.30 MN.10: 4 residues within 4Å: Chain D: E.10, D.12, D.21, H.26 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.10, D:D.12, D:D.21, D:H.26, H2O.40, H2O.40

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.12, Y.14, N.16, D.21 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.12, A:Y.14, A:D.21, H2O.9, H2O.10 CA.5: 4 residues within 4Å: Chain B: D.12, Y.14, N.16, D.21 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.12, B:Y.14, B:D.21, H2O.19, H2O.20 CA.8: 4 residues within 4Å: Chain C: D.12, Y.14, N.16, D.21 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.12, C:Y.14, C:D.21, H2O.29, H2O.29 CA.11: 4 residues within 4Å: Chain D: D.12, Y.14, N.16, D.21 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.12, D:Y.14, D:D.21, H2O.38, H2O.39

4 x XMM: 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside(Non-covalent)

XMM.3: 9 residues within 4Å: Chain A: Y.14, N.16, G.100, L.101, Y.102, A.209, D.210, G.229, R.230 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.16, A:G.100, A:L.101, A:Y.102, A:Y.102, A:Y.102, A:R.230 Water bridges: A:Y.14 XMM.6: 9 residues within 4Å: Chain B: Y.14, N.16, G.100, L.101, Y.102, A.209, D.210, G.229, R.230 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.16, B:G.100, B:L.101, B:Y.102, B:Y.102, B:R.230 XMM.9: 9 residues within 4Å: Chain C: Y.14, N.16, G.100, L.101, Y.102, A.209, D.210, G.229, R.230 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.16, C:G.100, C:L.101, C:Y.102, C:Y.102, C:R.230 XMM.12: 9 residues within 4Å: Chain D: Y.14, N.16, G.100, L.101, Y.102, A.209, D.210, G.229, R.230 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.16, D:G.100, D:L.101, D:Y.102, D:Y.102, D:Y.102, D:R.230 Water bridges: D:Y.14

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Nagano, C.S. et al., Insights Into the Structural Basis of the Ph- Dependent Dimer-Tetramer Equilibrium Through Crystallographic Analysis of Recombinant Diocleinae Lectins. Biochem.J. (2008)

Release Date

2007-10-30

Peptides

LECTIN ALPHA CHAIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

LECTIN ALPHA CHAIN