SMTL ID : 6x7j.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.97 Å

Oligo State

monomer

Ligands

1 x FUL: beta-L-fucopyranose(Non-covalent)

FUL.1: 12 residues within 4Å: Chain A: D.101, D.102, N.119, Q.120, S.121, D.146, Q.147, G.148, G.149, D.150 Ligands: CA.2, FUC.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.119 Hydrogen bonds: A:D.101, A:D.101, A:Q.147, A:D.150

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

CA.2: 8 residues within 4Å: Chain A: D.101, D.102, D.146, Q.147, G.148, D.150 Ligands: FUL.1, FUC.9 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.101, A:D.102, A:D.146, A:G.148, A:D.150 CA.3: 5 residues within 4Å: Chain A: G.55, T.56, Q.59, D.72, P.73 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.55, A:D.72, A:P.73, H2O.3, H2O.5 CA.4: 4 residues within 4Å: Chain A: Q.18, T.77, D.78, Q.147 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.78, A:Q.147, H2O.3, H2O.9, H2O.9 CA.5: 4 residues within 4Å: Chain A: Y.13, V.29, K.32, E.33 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:Y.13, A:V.29, A:K.32, H2O.9, H2O.9, H2O.10 CA.6: 1 residues within 4Å: Chain A: G.63 No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain A: G.110, P.112 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.110, H2O.1, H2O.6, H2O.9 CA.10: 2 residues within 4Å: Chain A: S.64, S.67 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.67, H2O.6, H2O.8, H2O.10, H2O.10

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

EDO.8: 3 residues within 4Å: Chain A: T.56, Q.59, E.60 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.56

1 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.9: 11 residues within 4Å: Chain A: D.101, D.102, N.119, Q.120, S.121, Q.147, G.148, G.149, D.150 Ligands: FUL.1, CA.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.119 Hydrogen bonds: A:Q.147, A:G.148, A:G.148, A:D.150 Water bridges: A:S.121

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

Related Entries With Identical Sequence