SMTL ID : 6x7y.1

N-acetyl-glucosamine-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 NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.1: 14 residues within 4Å: Chain A: R.47, D.101, D.102, N.119, Q.120, S.121, D.146, Q.147, G.148, G.149, D.150 Ligands: NAG.2, CA.3, EDO.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.102, A:Q.147, A:G.148, A:D.150 Water bridges: A:R.47

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.2: 14 residues within 4Å: Chain A: R.47, D.101, D.102, N.119, Q.120, S.121, D.146, Q.147, G.148, G.149, D.150 Ligands: NDG.1, CA.3, EDO.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.102, A:Q.147, A:G.148, A:D.150 Water bridges: A:R.47

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 8 residues within 4Å: Chain A: D.101, D.102, D.146, Q.147, G.148, D.150 Ligands: NDG.1, NAG.2 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.4: 4 residues within 4Å: Chain A: G.55, 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.2, H2O.4 CA.5: 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.7, H2O.7 CA.6: 4 residues within 4Å: Chain A: Y.13, V.29, K.32, E.33 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.13, A:V.29, A:K.32, H2O.7

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

EDO.7: 3 residues within 4Å: Chain A: T.56, Q.59, E.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.56 Water bridges: A:E.60 EDO.8: 6 residues within 4Å: Chain A: Q.147, G.148, G.149, D.150 Ligands: NDG.1, NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.147

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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