SMTL ID : 6x9m.1

3-O-methyl-glucose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

monomer

Ligands

5 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 7 residues within 4Å: Chain A: D.106, D.107, D.151, Q.152, G.153, D.155 Ligands: 3MG.7 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.106, A:D.107, A:D.151, A:G.153, A:D.155 CA.2: 4 residues within 4Å: Chain A: G.60, Q.64, D.77, P.78 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.60, A:D.77, A:P.78, H2O.2, H2O.5 CA.3: 4 residues within 4Å: Chain A: Q.23, T.82, D.83, Q.152 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.83, A:Q.152, H2O.1, H2O.8, H2O.9 CA.4: 4 residues within 4Å: Chain A: Y.18, V.34, K.37, E.38 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.18, A:V.34, A:K.37, H2O.9, H2O.9 CA.8: 1 residues within 4Å: Chain A: G.68 No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 3 residues within 4Å: Chain A: T.61, Q.64, E.65 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.65 EDO.6: 8 residues within 4Å: Chain A: I.113, N.114, N.116, V.118, F.135, T.136, I.137, S.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.113, A:N.114, A:T.136

1 x 3MG: 3-O-methyl-beta-D-glucopyranose(Non-covalent)

3MG.7: 11 residues within 4Å: Chain A: D.106, D.107, N.124, Q.125, S.126, D.151, Q.152, G.153, G.154, D.155 Ligands: CA.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.106, A:Q.152, A:G.153, A:D.155 Water bridges: A:S.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, S. et al., Structural Basis of Ligand Selectivity by a Bacterial Adhesin Lectin Involved in Multispecies Biofilm Formation. Mbio (2021)

Release Date

2021-06-02

Peptides

Antifreeze protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Antifreeze protein