SMTL ID : 6x8y.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

monomer

Ligands

1 x RIP: beta-D-ribopyranose(Non-covalent)

RIP.1: 10 residues within 4Å: Chain A: D.104, D.105, N.122, Q.123, S.124, Q.150, G.151, G.152, D.153 Ligands: CA.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.104, A:Q.123, A:Q.150, A:G.151, A:D.153

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.104, D.105, D.149, G.151, D.153 Ligands: RIP.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.104, A:D.105, A:D.149, A:G.151, A:D.153 CA.3: 3 residues within 4Å: Chain A: G.58, D.75, P.76 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.58, A:D.75, A:P.76, H2O.1, H2O.5 CA.4: 3 residues within 4Å: Chain A: Q.21, D.81, Q.150 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.81, A:Q.150, H2O.5, H2O.7, H2O.8 CA.5: 3 residues within 4Å: Chain A: Y.16, V.32, K.35 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:Y.16, A:V.32, A:K.35, H2O.8, H2O.8, H2O.8

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

EDO.6: 2 residues within 4Å: Chain A: T.59, Q.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.59 Water bridges: A:E.63 EDO.7: 3 residues within 4Å: Chain A: R.29, V.32, Y.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.29, A:Y.85 EDO.8: 4 residues within 4Å: Chain A: N.112, T.134, I.135, S.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.136, A:S.136 Water bridges: A:E.137

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