SMTL ID : 5j6y.1

Crystal structure of PA14 domain of MpAFP Antifreeze protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.03 Å

Oligo State

monomer

Ligands

8 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: GLC.9, BGC.10 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.3, H2O.9, H2O.9 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.70, H2O.6, H2O.6, H2O.9, H2O.10 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.5 CA.5: 4 residues within 4Å: Chain A: Q.2, 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.9, H2O.9, H2O.10 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.5, H2O.5, H2O.10

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.9: 10 residues within 4Å: Chain A: D.107, D.108, N.125, Q.126, Q.153, G.154, G.155, D.156 Ligands: CA.1, BGC.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.108, A:Q.153, A:D.156 Water bridges: A:D.156

1 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.10: 10 residues within 4Å: Chain A: D.107, D.108, N.125, Q.126, Q.153, G.154, G.155, D.156 Ligands: CA.1, GLC.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.108, A:Q.153, A:D.156 Water bridges: A:D.156

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Guo, S. et al., Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice. Sci Adv (2017)

Release Date

2017-06-07

Peptides

Antifreeze protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Antifreeze protein