SMTL ID : 6x7t.1

Allose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

monomer

Ligands

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

CA.1: 8 residues within 4Å: Chain A: D.109, D.110, D.154, Q.155, G.156, D.158 Ligands: VDS.7, VDV.8 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.109, A:D.110, A:D.154, A:G.156, A:D.158 CA.2: 4 residues within 4Å: Chain A: G.63, Q.67, D.80, P.81 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.63, A:D.80, A:P.81, H2O.2, H2O.5 CA.3: 4 residues within 4Å: Chain A: Q.26, T.85, D.86, Q.155 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.86, A:Q.155, H2O.1, H2O.8, H2O.8 CA.4: 5 residues within 4Å: Chain A: Y.21, V.37, D.38, K.40, E.41 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:Y.21, A:V.37, A:K.40, H2O.8, H2O.8, H2O.9 CA.5: 2 residues within 4Å: Chain A: S.72, S.75 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.72, A:S.75, H2O.4, H2O.9, H2O.9 CA.6: 1 residues within 4Å: Chain A: G.71 No protein-ligand interaction detected (PLIP)

1 x VDS: beta-D-allofuranose(Non-covalent)

VDS.7: 11 residues within 4Å: Chain A: D.109, D.110, N.127, Q.128, S.129, Q.155, G.156, G.157, D.158 Ligands: CA.1, VDV.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.129, A:S.129, A:Q.155, A:G.156, A:D.158 Water bridges: A:N.127, A:N.127

1 x VDV: alpha-D-allofuranose(Non-covalent)

VDV.8: 11 residues within 4Å: Chain A: D.109, D.110, N.127, Q.128, S.129, Q.155, G.156, G.157, D.158 Ligands: CA.1, VDS.7 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.109, A:S.129, A:S.129, A:Q.155, A:G.156, A:G.156, A:D.158 Water bridges: A:N.127, A:N.127

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