SMTL ID : 3rrd.1

Native structure of Dioclea virgata lectin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.46 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 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24, H2O.3 MN.3: 4 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24, H2O.6 MN.5: 4 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24, H2O.9 MN.7: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24, H2O.12

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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.10, A:D.10, A:Y.12, A:D.19, H2O.3 CA.4: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.10, B:D.10, B:Y.12, B:D.19, H2O.6 CA.6: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.10, C:D.10, C:Y.12, C:D.19, H2O.9 CA.8: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.10, D:D.10, D:Y.12, D:D.19, H2O.12

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Batista da Nobrega, R. et al., Structure of Dioclea virgata lectin: Relations between carbohydrate binding site and nitric oxide production. Biochimie (2012)

Release Date

2011-11-09

Peptides

Lectin alpha chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Lectin alpha chain

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