SMTL ID : 6rhh.1

Single crystal serial study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from Steccherinum murashkinskyi at sub-atomic resolution. Third structure of the series with 315 KGy dose.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.97 Å

Oligo State

monomer

Ligands

2 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: 9 residues within 4Å: Chain A: R.323, G.324, V.331, E.385, A.387, P.389, G.434, D.435, N.436 No protein-ligand interaction detected (PLIP) NAG-NAG.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.418, A:N.421

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

CU.3: 10 residues within 4Å: Chain A: H.65, H.110, H.112, H.400, H.402, F.450, H.452 Ligands: CU.4, CU.5, OXY.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.112, A:H.402, A:H.452, H2O.1, H2O.1 CU.4: 8 residues within 4Å: Chain A: H.65, H.67, H.110, H.400, H.454 Ligands: CU.3, CU.5, OXY.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.67, A:H.110, A:H.454, H2O.1, H2O.1 CU.5: 8 residues within 4Å: Chain A: H.65, H.67, G.68, H.400, H.402 Ligands: CU.3, CU.4, OXY.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.65, A:H.400, H2O.1, H2O.19 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 OXY: OXYGEN MOLECULE(Non-covalent)

OXY.7: 11 residues within 4Å: Chain A: H.65, H.67, H.110, H.112, H.400, H.402, H.452, H.454 Ligands: CU.3, CU.4, CU.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.67

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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