SMTL ID : 6x8a.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.06 Å

Oligo State

monomer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 10 residues within 4Å: Chain A: D.107, D.108, N.125, Q.126, S.127, Q.153, G.154, G.155, D.156 Ligands: CA.2 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.156, A:D.156 Hydrogen bonds: A:D.107, A:Q.153, A:D.156

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

CA.2: 6 residues within 4Å: Chain A: D.107, D.108, D.152, G.154, D.156 Ligands: GLC-FRU.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.107, A:D.108, A:D.152, A:G.154, A:D.156 CA.3: 3 residues within 4Å: Chain A: Q.24, D.84, Q.153 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.84, A:Q.153, H2O.3, H2O.7, H2O.8 CA.4: 2 residues within 4Å: Chain A: S.70, S.73 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.73, H2O.5, H2O.6, H2O.7, H2O.8 CA.5: 3 residues within 4Å: Chain A: G.61, D.78, P.79 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.61, A:D.78, A:P.79, H2O.2, H2O.5 CA.6: 4 residues within 4Å: Chain A: Q.2, D.4, T.6, D.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.4, A:T.6, A:D.8, A:D.8, H2O.1 CA.7: 3 residues within 4Å: Chain A: Y.19, V.35, K.38 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.19, A:V.35, A:K.38, H2O.8, H2O.8 CA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

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