SMTL ID : 4x4k.1

Structure of laccase from Botrytis aclada with full copper content

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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.1: 12 residues within 4Å: Chain A: M.89, H.118, N.119, S.209, F.211, E.212, D.215, W.415, F.573, A.574, D.576 Ligands: NAG.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.209, A:D.215 Water bridges: A:D.215

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.2: 12 residues within 4Å: Chain A: R.68, E.69, Y.70, P.96, I.184, V.197, G.198, V.199, I.200, N.231, F.253, L.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.67, A:E.69, A:Y.70

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

CU.3: 5 residues within 4Å: Chain A: H.463, C.526, I.528, H.531, L.536 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.463, A:C.526, A:H.531 CU.4: 5 residues within 4Å: Chain A: H.170, H.466, H.468, H.525 Ligands: CU.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.170, A:H.468, A:H.525, H2O.5 CU.5: 4 residues within 4Å: Chain A: H.126, W.166, H.168, H.527 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.126, A:H.168, A:H.527, H2O.5 CU.6: 6 residues within 4Å: Chain A: H.124, H.126, G.127, H.466, H.468 Ligands: CU.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.124, A:H.466, H2O.2 CU.7: 2 residues within 4Å: Chain A: E.117, H.118 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.118

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

NAG.8: 3 residues within 4Å: Chain A: W.71, S.73, N.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.71, A:N.92 NAG.9: 6 residues within 4Å: Chain A: N.76, M.89, E.117, H.118, N.119 Ligands: NAG-NAG-BMA.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.119 Hydrogen bonds: A:N.76, A:E.117, A:H.118 NAG.10: 4 residues within 4Å: Chain A: D.391, E.392, Q.393, N.407 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.392 Hydrogen bonds: A:D.391, A:D.391, A:D.391, A:N.407 Water bridges: A:D.391 NAG.11: 3 residues within 4Å: Chain A: F.424, N.425, N.426 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.424, A:N.425 NAG.12: 3 residues within 4Å: Chain A: D.237, A.341, N.342 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.237, A:D.237

1 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.13: 4 residues within 4Å: Chain A: Y.298, P.372, A.374, S.375 No protein-ligand interaction detected (PLIP)

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.14: 2 residues within 4Å: Chain A: R.327, S.359 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.327

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipov, E.M. et al., Incorporation of copper ions into crystals of T2 copper-depleted laccase from Botrytis aclada. Acta Crystallogr.,Sect.F (2015)

Release Date

2015-12-09

Peptides

Laccase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Laccase

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