SMTL ID : 7wis.1

Catalytic intermediate structure of N381A mutant of copper amine oxidase from Arthrobacter globiformis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

CU.1: 3 residues within 4Å: Chain A: H.423, H.425, H.584 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.423, A:H.425, A:H.584, H2O.3, H2O.17 CU.8: 3 residues within 4Å: Chain B: H.423, H.425, H.584 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.423, B:H.425, B:H.584

2 x HY1: PHENYLACETALDEHYDE(Non-covalent)

HY1.2: 9 residues within 4Å: Chain A: F.97, A.127, P.128, L.129, W.160, Y.288, G.372 Chain B: L.350, W.351 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.97, A:A.127, A:P.128, A:L.129, A:W.160, A:W.160, B:L.350, B:W.351 Hydrogen bonds: A:Y.288 Water bridges: A:A.373 HY1.9: 7 residues within 4Å: Chain A: L.350, W.351 Chain B: A.127, P.128, L.129, W.160, G.372 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.127, B:P.128, B:L.129, B:W.160, B:W.160, A:L.350, A:W.351 Water bridges: B:G.372, B:A.373

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: E.339, R.362, K.393 Chain B: D.340, W.341, G.342 Ligands: GOL.6 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.362, A:K.393, A:K.393 Water bridges: A:E.339, A:E.339, A:Y.381, A:K.393, B:D.340, B:D.340, B:R.359 GOL.4: 7 residues within 4Å: Chain A: R.611, S.612, P.613, V.614, L.615, D.616 Chain B: T.202 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Water bridges: B:T.202, A:D.616 Hydrogen bonds: A:R.611, A:P.613, A:L.615, A:D.616 GOL.5: 7 residues within 4Å: Chain A: W.341, N.360, Y.383, D.385, T.387, E.389, K.602 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.341, A:N.360, A:D.385, A:K.602, A:K.602 Water bridges: A:D.385, A:D.385 GOL.6: 7 residues within 4Å: Chain A: W.341, R.362, Y.381, E.389, E.391 Chain B: W.341 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.362, A:R.362, A:Y.381 GOL.7: 7 residues within 4Å: Chain A: H.507, K.602, R.604 Chain B: Q.511, L.582, D.597, T.598 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.511, A:H.507, A:K.602, A:K.602 Water bridges: B:Q.511, B:T.598, A:R.604 GOL.10: 7 residues within 4Å: Chain B: W.341, N.360, Y.383, D.385, T.387, E.389, K.602 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.360 Water bridges: B:N.360, B:D.385, B:D.385, B:T.387 GOL.11: 7 residues within 4Å: Chain A: D.340, W.341, G.342 Chain B: E.339, R.362, E.391, K.393 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.362, B:K.393, B:K.393, A:D.340 Water bridges: B:E.339, B:Y.381, B:K.393 GOL.12: 11 residues within 4Å: Chain B: R.524, R.525, P.545, T.546, F.549, V.550, H.553, S.554, G.555, G.556, A.557 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.524, B:F.549, B:A.557, B:A.557

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shoji, M. et al., Molecular mechanism of a large conformational change of the quinone cofactor in the semiquinone intermediate of bacterial copper amine oxidase. Chem Sci (2022)

Release Date

2022-11-16

Peptides

Phenylethylamine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phenylethylamine oxidase

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