SMTL ID : 5nq8.1

Crystal structure of laccases from Pycnoporus sanguineus, izoform II

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

NAG-NAG-MAN.1: 9 residues within 4Å: Chain A: R.43, E.44, N.75, M.78, H.174, V.175, A.176, L.179 Ligands: MLI.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.43, A:A.176 Hydrogen bonds: A:A.176

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: P.346, L.347, N.348, S.404, P.406, N.455 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.346

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

CU.3: 5 residues within 4Å: Chain A: H.416, C.472, I.474, H.477, F.482 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.416, A:C.472, A:H.477 CU.4: 5 residues within 4Å: Chain A: H.85, H.87, H.419, H.421 Ligands: PER.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.85, A:H.419, H2O.14 CU.5: 6 residues within 4Å: Chain A: H.85, H.87, W.128, H.130, H.473 Ligands: PER.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.87, A:H.130, A:H.473 CU.6: 5 residues within 4Å: Chain A: H.132, H.419, H.421, H.471 Ligands: PER.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.132, A:H.421, A:H.471

1 x PER: PEROXIDE ION(Non-covalent)

PER.7: 11 residues within 4Å: Chain A: H.85, H.87, H.130, H.132, H.419, H.421, H.471, H.473 Ligands: CU.4, CU.5, CU.6 No protein-ligand interaction detected (PLIP)

2 x ME2: 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE(Non-covalent)

ME2.8: 7 residues within 4Å: Chain A: P.25, V.26, G.62, D.63, R.64, Q.66, Q.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.64 ME2.9: 3 residues within 4Å: Chain A: P.498, V.499, P.500 No protein-ligand interaction detected (PLIP)

1 x IPH: PHENOL(Non-covalent)

IPH.10: 1 residues within 4Å: Chain A: F.353 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.353 Water bridges: A:P.184

2 x NA: SODIUM ION(Non-functional Binders)

NA.11: 2 residues within 4Å: Chain A: A.124, S.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.124, A:A.124 NA.12: 4 residues within 4Å: Chain A: A.22, I.23, G.24, S.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.23, A:S.58 Water bridges: A:S.58

3 x MLI: MALONATE ION(Non-functional Binders)

MLI.13: 4 residues within 4Å: Chain A: N.75, H.76, T.77 Ligands: NAG-NAG-MAN.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.76, A:T.77, A:T.77 MLI.14: 3 residues within 4Å: Chain A: Q.213, P.274, V.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.213, A:Q.213, A:V.275 MLI.15: 5 residues within 4Å: Chain A: H.363, A.383, G.390, V.392, Y.393 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.363, A:V.392, A:Y.393 Water bridges: A:V.394

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Orlikowska, M. et al., Structural studies of two thermostable laccases from the white-rot fungus Pycnoporus sanguineus. Int. J. Biol. Macromol. (2018)

Release Date

2017-11-01

Peptides

Laccase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Laccase

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