SMTL ID : 6ri4.1

Single crystal serial study of the inhibition of laccases from Steccherinum murashkinskyi by fluoride anions at sub-atomic resolution. First structure of the series with 13 KGy dose.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.08 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: R.323, G.324, V.331, E.385, A.387, P.389, D.435, N.436 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: V.305, T.307, N.414, T.416, P.417, N.418 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.416 Water bridges: A:N.421, A:N.421

4 x CU: COPPER (II) ION(Non-covalent)

CU.3: 6 residues within 4Å: Chain A: H.110, H.112, H.400, H.402, F.450, H.452 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.112, A:H.402, A:H.452, H2O.2, H2O.11 CU.4: 6 residues within 4Å: Chain A: H.65, H.67, W.108, H.110, A.244, H.454 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.67, A:H.110, A:H.454, H2O.2, H2O.11 CU.5: 6 residues within 4Å: Chain A: H.65, H.67, G.68, H.400, H.402 Ligands: F.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.65, A:H.400, H2O.2, H2O.2 CU.6: 6 residues within 4Å: Chain A: H.397, P.398, C.453, I.455, H.458, F.463 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.397, A:C.453, A:H.458

1 x F: FLUORIDE ION(Non-covalent)

F.7: 7 residues within 4Å: Chain A: H.65, H.67, G.68, H.400, H.402, G.403 Ligands: CU.5 No protein-ligand interaction detected (PLIP)

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.8: 9 residues within 4Å: Chain A: L.69, F.70, Q.71, K.72, F.98, N.99, V.100, P.101, Q.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.70, A:Q.71 Water bridges: A:K.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Polyakov, K.M. et al., The subatomic resolution study of laccase inhibition by chloride and fluoride anions using single-crystal serial crystallography: insights into the enzymatic reaction mechanism. Acta Crystallogr D Struct Biol (2019)

Release Date

2019-05-01

Peptides

Laccase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Laccase 2

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