SMTL ID : 5or3.1 (1 other biounit)

Crystal structure of Aspergillus oryzae catechol oxidase in met/deoxy-form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

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: 13 residues within 4Å: Chain A: T.83, H.86, L.87, A.88, A.100, T.101, N.104, L.230, G.358, Y.359 Chain B: H.86, P.89, N.228 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.86 Water bridges: A:H.86

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.2: 11 residues within 4Å: Chain A: N.228 Chain B: T.83, H.86, L.87, A.88, A.100, T.101, N.104, L.230, G.358, Y.359 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.228

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

CU.3: 5 residues within 4Å: Chain A: H.102, I.109, H.110, H.119, F.308 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.102, A:H.110, A:H.119, H2O.9 CU.4: 5 residues within 4Å: Chain A: H.284, H.288, F.308, H.311, H.312 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.284, A:H.288, A:H.312, H2O.9 CU.13: 6 residues within 4Å: Chain B: H.102, I.109, H.110, W.118, H.119, F.308 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.102, B:H.110, B:H.119, H2O.16 CU.14: 5 residues within 4Å: Chain B: H.284, H.288, F.308, H.311, H.312 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.284, B:H.288, B:H.312, H2O.16

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

MAN.5: 5 residues within 4Å: Chain A: T.14, A.15, D.150, Q.247, F.252 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.247 MAN.9: 1 residues within 4Å: Chain A: T.5 No protein-ligand interaction detected (PLIP) MAN.15: 8 residues within 4Å: Chain B: S.12, S.13, T.14, A.149, D.150, Q.247, T.251, P.253 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.12, B:D.150, B:T.251 Water bridges: B:D.150

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

NAG.6: 5 residues within 4Å: Chain A: L.6, Q.23, N.26, F.27, N.30 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.27 Hydrogen bonds: A:N.26, A:N.30 NAG.7: 3 residues within 4Å: Chain A: P.219, G.220, N.222 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.222 Water bridges: A:N.222 NAG.8: 7 residues within 4Å: Chain A: S.346, P.347, N.348 Chain B: L.181, G.221, N.222, M.223 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:M.223 Water bridges: B:M.223, A:N.348, A:N.348 NAG.16: 5 residues within 4Å: Chain B: L.6, Q.23, N.26, F.27, N.30 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.27 Hydrogen bonds: B:N.30 NAG.17: 3 residues within 4Å: Chain B: P.219, G.220, N.222 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.222 NAG.18: 7 residues within 4Å: Chain A: L.181, G.221, N.222, M.223 Chain B: S.346, P.347, N.348 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:G.220, B:N.348

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 8 residues within 4Å: Chain A: I.172, P.173, N.174, Q.175, P.192, G.193, S.194 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.174, A:Q.175, A:G.193 EDO.11: 6 residues within 4Å: Chain A: D.177, D.189, L.190, P.191, E.244, R.248 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.248, A:R.248 Water bridges: A:D.177 EDO.12: 4 residues within 4Å: Chain A: N.174, Q.175, G.176 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.175

Links

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Citation

Penttinen, L. et al., A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes. PLoS ONE (2018)

Release Date

2018-05-09

Peptides

catechol oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

catechol oxidase

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