SMTL ID : 4j3p.1

Crystal structure of full-length catechol oxidase from Aspergillus oryzae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 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(Non-covalent)

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: T.83, L.87, N.104, Y.359 Chain B: H.86, N.228 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.86, B:N.228 Water bridges: A:H.86 Hydrophobic interactions: B:N.228 NAG-NAG-BMA.10: 6 residues within 4Å: Chain A: H.86, N.228 Chain B: T.83, L.87, N.104, Y.359 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.86, A:N.228 Water bridges: B:H.86 Hydrophobic interactions: A:N.228

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

CU.2: 4 residues within 4Å: Chain A: H.102, H.110, H.119 Ligands: OXY.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.102, A:H.110, A:H.119 CU.3: 5 residues within 4Å: Chain A: H.284, H.288, F.308, H.312 Ligands: OXY.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.284, A:H.288, A:H.312 CU.11: 4 residues within 4Å: Chain B: H.102, H.110, H.119 Ligands: OXY.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.102, B:H.110, B:H.119 CU.12: 5 residues within 4Å: Chain B: H.284, H.288, F.308, H.312 Ligands: OXY.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.284, B:H.288, B:H.312

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.4: 10 residues within 4Å: Chain A: H.102, H.110, H.119, H.284, H.288, S.302, F.308, H.312 Ligands: CU.2, CU.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.302 OXY.13: 10 residues within 4Å: Chain B: H.102, H.110, H.119, H.284, H.288, S.302, F.308, H.312 Ligands: CU.11, CU.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.302

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

NAG.5: 5 residues within 4Å: Chain A: L.6, Q.23, N.26, F.27, N.30 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.6, A:F.27 Hydrogen bonds: A:N.30 Water bridges: A:N.26, A:N.26 NAG.6: 4 residues within 4Å: Chain A: S.335, N.348 Chain B: G.221, N.222 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.335, A:N.348 Water bridges: A:S.335, A:G.336, A:N.348, B:G.221 NAG.7: 1 residues within 4Å: Chain A: N.222 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.222 NAG.14: 5 residues within 4Å: Chain B: L.6, Q.23, N.26, F.27, N.30 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.6, B:F.27 Hydrogen bonds: B:N.30 Water bridges: B:N.26, B:N.26 NAG.15: 4 residues within 4Å: Chain A: G.221, N.222 Chain B: S.335, N.348 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.335, B:N.348 Water bridges: B:S.335, B:G.336, B:N.348, A:G.221 NAG.16: 1 residues within 4Å: Chain B: N.222 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.222

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

MAN.8: 4 residues within 4Å: Chain A: T.14, A.149, D.150, T.251 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:T.14, A:T.14, A:A.149, A:T.251 MAN.17: 4 residues within 4Å: Chain B: T.14, A.149, D.150, T.251 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.150 Water bridges: B:T.14, B:T.14, B:A.149

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

SO4.9: 2 residues within 4Å: Chain A: S.62, K.63 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.63 SO4.18: 2 residues within 4Å: Chain B: S.62, K.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hakulinen, N. et al., The crystal structure of an extracellular catechol oxidase from the ascomycete fungus Aspergillus oryzae. J.Biol.Inorg.Chem. (2013)

Release Date

2013-11-27

Peptides

Catechol oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Catechol oxidase

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