SMTL ID : 3x40.1 (1 other biounit)

Copper amine oxidase from Arthrobacter globiformis: Product Schiff-base form produced by anaerobic reduction in the presence of sodium chloride

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.423, H.425, H.584 Ligands: CL.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.423, A:H.425, A:H.584, H2O.22 CU.11: 4 residues within 4Å: Chain B: H.423, H.425, H.584 Ligands: CL.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.423, B:H.425, B:H.584, H2O.44

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: Y.374, H.423, H.425, H.584, M.594 Ligands: CU.1 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: C.309, H.337, S.366, Y.379 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain B: Y.374, H.423, H.425, H.584, M.594 Ligands: CU.11 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: C.309, H.337, S.366, Y.379 Ligand excluded by PLIP

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

NA.4: 4 residues within 4Å: Chain A: A.85, A.86, R.140, S.554 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.140, A:S.554 NA.5: 6 residues within 4Å: Chain A: R.41, D.432, M.433, F.438, D.573, I.574 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.41, A:M.433, A:I.574 NA.14: 4 residues within 4Å: Chain B: A.85, A.86, R.140, S.554 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.85, B:R.140 NA.15: 6 residues within 4Å: Chain B: R.41, D.432, M.433, F.438, D.573, I.574 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.41, B:D.432, B:D.573, B:I.574

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: D.340, W.341, G.342 Chain B: E.339, R.362, E.391, K.393 Ligands: GOL.20 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.339, B:R.362, B:E.391, B:K.393 Water bridges: B:Y.381, A:D.340, A:D.340 GOL.7: 4 residues within 4Å: Chain A: H.507, K.602, R.604 Chain B: D.597 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:K.602, B:D.597 Water bridges: A:K.602, B:Q.511, B:Q.511, B:T.583, B:D.597, B:T.598 GOL.8: 5 residues within 4Å: Chain B: D.153, H.162, V.189, P.190, A.191 No protein-ligand interaction detected (PLIP) GOL.9: 10 residues within 4Å: Chain A: I.31, A.32, Y.33, L.34, V.243, Q.298, I.320, S.321, D.322, A.323 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.34, A:S.321, A:D.322 Water bridges: A:Q.298 GOL.10: 7 residues within 4Å: Chain A: W.341, R.362, Y.381, E.389, E.391 Ligands: GOL.16, GOL.20 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.362, A:E.389 Water bridges: A:E.389, A:E.391, A:K.393 GOL.16: 8 residues within 4Å: Chain A: E.339, R.362, E.391, K.393 Chain B: D.340, W.341, G.342 Ligands: GOL.10 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:D.340 Hydrogen bonds: A:E.339, A:R.362, A:E.391, A:K.393 GOL.17: 4 residues within 4Å: Chain A: D.597 Chain B: H.507, K.602, R.604 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.597, B:K.602 Water bridges: A:Q.511, A:Q.511, A:T.583, A:D.597, A:T.598, B:H.507, B:K.602 GOL.18: 5 residues within 4Å: Chain A: D.153, H.162, V.189, P.190, A.191 No protein-ligand interaction detected (PLIP) GOL.19: 10 residues within 4Å: Chain B: I.31, A.32, Y.33, L.34, V.243, Q.298, I.320, S.321, D.322, A.323 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.34, B:S.321, B:D.322 Water bridges: B:Q.298 GOL.20: 7 residues within 4Å: Chain B: W.341, R.362, Y.381, E.389, E.391 Ligands: GOL.6, GOL.10 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.362, B:E.389 Water bridges: B:K.393, A:W.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murakawa, T. et al., Probing the Catalytic Mechanism of Copper Amine Oxidase from Arthrobacter globiformis with Halide Ions. J.Biol.Chem. (2015)

Release Date

2015-08-19

Peptides

Phenylethylamine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Phenylethylamine oxidase

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