SMTL ID : 7wir.1

Holo form of N381A mutant of copper amine oxidase from Arthrobacter globiformis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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.11, H2O.20 CU.15: 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.45, H2O.50

30 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: H.507, K.602, R.604 Chain B: L.582, D.597 Ligands: GOL.16, GOL.23 Ligand excluded by PLIP GOL.3: 6 residues within 4Å: Chain A: E.339, R.362, K.393 Chain B: D.340, W.341, G.342 Ligand excluded by PLIP GOL.4: 9 residues within 4Å: Chain A: I.31, A.32, Y.33, L.34, V.243, Q.298, I.320, S.321, D.322 Ligand excluded by PLIP GOL.5: 9 residues within 4Å: Chain A: Q.511, P.512, T.583, F.585 Chain B: E.445, G.484, T.486, K.505, H.507 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: L.582, D.597 Chain B: H.507, K.602, R.604 Ligands: GOL.9 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: T.513, L.514, L.515, T.530, K.531 Chain B: R.449, R.482 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: N.360, Y.383, D.385, T.387, E.389, K.602 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: H.584, F.585, R.587, D.590, D.597 Chain B: R.604 Ligands: GOL.6 Ligand excluded by PLIP GOL.10: 8 residues within 4Å: Chain A: R.611, S.612, P.613, V.614, L.615, D.616 Chain B: L.201, T.202 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: S.463, R.464 Chain B: S.408, D.409, F.422 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: T.530, K.531, W.534, P.560 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain A: A.127, P.128, L.129, W.160, G.372 Chain B: L.350, W.351 Ligands: GOL.14 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain A: F.97, A.127, P.128, L.129, Y.294, G.372 Ligands: GOL.13 Ligand excluded by PLIP GOL.16: 10 residues within 4Å: Chain A: E.445, G.484, T.486, K.505, H.507 Chain B: Q.511, P.512, T.583, F.585 Ligands: GOL.2 Ligand excluded by PLIP GOL.17: 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 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain A: D.340, W.341 Chain B: E.339, R.362, K.393 Ligands: GOL.29 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain B: V.151, D.153, H.162, V.189, P.190, A.191 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain B: N.360, Y.383, D.385, T.387, K.602 Ligands: GOL.30 Ligand excluded by PLIP GOL.21: 10 residues within 4Å: Chain B: I.31, A.32, Y.33, L.34, V.243, L.295, Q.298, I.320, S.321, D.322 Ligand excluded by PLIP GOL.22: 9 residues within 4Å: Chain B: R.441, E.443, R.466, I.488, S.490, P.501, G.503, E.606, G.607 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain A: R.604 Chain B: H.584, F.585, R.587, D.590, D.597 Ligands: GOL.2 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain B: E.94, F.97, Y.299, T.370, I.371, G.372 Ligand excluded by PLIP GOL.25: 8 residues within 4Å: Chain A: L.201, T.202 Chain B: R.611, S.612, P.613, V.614, L.615, D.616 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain A: R.449, R.482 Chain B: T.513, L.514, T.530, K.531 Ligand excluded by PLIP GOL.27: 10 residues within 4Å: Chain B: A.7, L.34, G.35, V.36, F.241, D.242, V.243, V.319, I.320 Ligands: GOL.31 Ligand excluded by PLIP GOL.28: 2 residues within 4Å: Chain B: R.63, E.81 Ligand excluded by PLIP GOL.29: 8 residues within 4Å: Chain A: W.341 Chain B: W.341, R.362, Y.381, E.389, E.391 Ligands: GOL.18, GOL.30 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain B: W.341, Y.383, E.389, K.602 Ligands: GOL.20, GOL.29 Ligand excluded by PLIP GOL.31: 9 residues within 4Å: Chain B: V.36, D.38, G.240, F.241, D.242, V.248, H.250, R.266 Ligands: GOL.27 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain B: D.38, E.245, R.266, R.430, D.540, R.543 Ligand excluded by PLIP

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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