SMTL ID : 6x7x.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

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

CA.1: 7 residues within 4Å: Chain A: D.107, D.108, D.152, G.154, D.156 Ligands: MAN.10, BMA.11 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.2: 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.1, H2O.7, H2O.8 CA.3: 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.4, H2O.7, H2O.8, H2O.8 CA.4: 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.4 CA.5: 5 residues within 4Å: Chain A: Q.2, D.3, D.4, T.6, D.8 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.4, A:T.6, A:D.8, H2O.1, H2O.1 CA.6: 3 residues within 4Å: Chain A: Y.19, V.35, K.38 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:Y.19, A:V.35, A:K.38, H2O.8, H2O.8, H2O.8 CA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.8: 1 residues within 4Å: Chain A: S.169 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.169, H2O.6, H2O.8, H2O.10 CA.13: 1 residues within 4Å: Chain A: A.165 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.165, H2O.5, H2O.9

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

EDO.9: 4 residues within 4Å: Chain A: D.41, G.80, D.81, N.82 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.41, A:G.80, A:N.82 Water bridges: A:D.81 EDO.12: 6 residues within 4Å: Chain A: Q.24, N.26, N.125, Q.153 Ligands: MAN.10, BMA.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.125 Water bridges: A:Q.24, A:Q.153

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.10: 11 residues within 4Å: Chain A: D.107, D.108, Q.126, S.127, Q.153, G.154, G.155, D.156 Ligands: CA.1, BMA.11, EDO.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.108, A:Q.153, A:D.156 Water bridges: A:V.128

1 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.11: 12 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.1, MAN.10, EDO.12 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.107, A:D.108, A:Q.126, A:Q.153, A:G.154, A:D.156

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