SMTL ID : 7ynh.2 (1 other biounit)

Catalytic intermediate of copper amine oxidase determined by serial femtosecond X-ray crystallography using a single-flow liquid jet system

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: R.41, D.432, M.433, D.573, I.574 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.41, A:D.432, A:D.573, A:I.574 NA.4: 5 residues within 4Å: Chain B: R.41, D.432, M.433, D.573, I.574 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.41, B:I.574, B:I.574

2 x HY1: PHENYLACETALDEHYDE(Non-covalent)

HY1.2: 10 residues within 4Å: Chain A: A.127, P.128, L.129, Y.288, D.290, Y.294, I.371, G.372, N.373, Y.374 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.127, A:L.129, A:Y.288 HY1.5: 10 residues within 4Å: Chain B: A.127, P.128, L.129, Y.288, D.290, Y.294, I.371, G.372, N.373, Y.374 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.127, B:L.129, B:Y.288

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

CU.3: 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.9, H2O.13 CU.6: 3 residues within 4Å: Chain B: H.423, H.425, H.584 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.423, B:H.425, B:H.584, H2O.26, H2O.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murakawa, T. et al., Serial femtosecond X-ray crystallography of an anaerobically formed catalytic intermediate of copper amine oxidase. Acta Crystallogr D Struct Biol (2022)

Release Date

2022-11-16

Peptides

Phenylethylamine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Phenylethylamine oxidase

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