SMTL ID : 3wa3.1 (1 other biounit)

Crystal structure of copper amine oxidase from arthrobacter globiformis in N2 condition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 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.14, H2O.14 CU.24: 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.46, H2O.46

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

NA.2: 6 residues within 4Å: Chain A: R.41, D.432, M.433, F.438, D.573, I.574 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.41, A:M.433, A:D.573, A:I.574 NA.25: 6 residues within 4Å: Chain B: R.41, D.432, M.433, F.438, D.573, I.574 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.41, B:D.573, B:I.574

6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 5 residues within 4Å: Chain A: T.184, V.186, F.187, E.405 Ligands: PEG.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.405 PGE.4: 4 residues within 4Å: Chain A: H.193, E.200, L.201 Chain B: R.611 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.193 PGE.5: 6 residues within 4Å: Chain A: S.463, R.464, R.466 Chain B: S.408, D.409 Ligands: EDO.38 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Water bridges: A:R.464, A:R.466, A:E.500, A:E.500 Hydrogen bonds: B:S.408 PGE.26: 5 residues within 4Å: Chain B: T.184, V.186, F.187, E.405 Ligands: PEG.42 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.405, B:E.405 Water bridges: B:T.184 PGE.27: 4 residues within 4Å: Chain A: R.611 Chain B: H.193, E.200, L.201 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.193, B:E.200 PGE.28: 6 residues within 4Å: Chain A: S.408, D.409 Chain B: S.463, R.464, R.466 Ligands: EDO.15 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:R.464, B:R.466, B:E.500 Hydrogen bonds: A:S.408, A:D.409

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 3 residues within 4Å: Chain A: N.118, L.119, D.120 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.120, A:V.121 PG4.7: 15 residues within 4Å: Chain A: F.97, A.127, P.128, W.160, Y.288, Y.294, I.371, G.372, N.373, Y.374, F.399 Chain B: D.349, L.350, W.351 Ligands: PEG.17 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.373, B:D.349, B:L.350, B:W.351 Water bridges: A:G.372, A:G.372 PG4.29: 3 residues within 4Å: Chain B: N.118, L.119, D.120 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.120, B:V.121 PG4.30: 15 residues within 4Å: Chain A: D.349, L.350, W.351 Chain B: F.97, A.127, P.128, W.160, Y.288, Y.294, I.371, G.372, N.373, Y.374, F.399 Ligands: PEG.40 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.349, A:L.350, A:W.351, B:N.373 Water bridges: B:G.372, B:G.372

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 7 residues within 4Å: Chain A: V.181, I.182, D.183, T.184, G.185 Ligands: EDO.12, EDO.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.183 Water bridges: A:R.117 1PE.31: 7 residues within 4Å: Chain B: V.181, I.182, D.183, T.184, G.185 Ligands: EDO.35, EDO.39 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.183 Water bridges: B:R.117, B:D.183

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

EDO.9: 8 residues within 4Å: Chain A: Y.33, G.35, V.36, L.37, R.53, R.543, Y.544 Ligands: PEG.22 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: G.406, G.407, S.408, D.409 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: G.455, N.456, E.457 Chain B: P.279 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: I.182 Ligands: 1PE.8 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: N.355, Y.356, R.358 Chain B: T.197 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: G.35, V.36, F.241, D.242 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: D.409 Chain B: S.463, R.464, K.465 Ligands: PGE.28 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: R.109, R.180, V.181 Ligands: 1PE.8 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain B: Y.33, G.35, V.36, L.37, R.53, R.543, Y.544 Ligands: PEG.45 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain B: G.406, G.407, S.408, D.409 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain A: P.279 Chain B: G.455, N.456, E.457 Ligand excluded by PLIP EDO.35: 2 residues within 4Å: Chain B: I.182 Ligands: 1PE.31 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain A: T.197 Chain B: N.355, Y.356, R.358 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain B: G.35, V.36, F.241, D.242 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain A: S.463, R.464, K.465 Chain B: D.409 Ligands: PGE.5 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain B: R.109, R.180, V.181 Ligands: 1PE.31 Ligand excluded by PLIP

12 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.17: 10 residues within 4Å: Chain A: L.93, E.94, F.97, P.128, Y.294, Y.299, T.370, I.371, G.372 Ligands: PG4.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.94, A:T.370, A:G.372 PEG.18: 3 residues within 4Å: Chain B: E.478, D.480, R.485 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.480, B:R.485, B:R.485 Water bridges: B:R.477, B:E.478, B:D.480 PEG.19: 5 residues within 4Å: Chain A: F.187, P.188, P.404, E.405 Ligands: PGE.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.405 PEG.20: 7 residues within 4Å: Chain A: L.582, H.584, F.585, R.587, D.590, D.597 Chain B: R.604 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.604, B:R.604, A:F.585, A:R.587 Water bridges: A:F.585 PEG.21: 7 residues within 4Å: Chain A: W.341, R.362, Y.381, E.391, K.393 Chain B: W.341, G.342 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.362, A:R.362, A:E.389, A:K.393 Water bridges: A:Y.381, B:R.359 PEG.22: 8 residues within 4Å: Chain A: D.38, E.245, R.266, Y.538, D.540, R.543, Y.544 Ligands: EDO.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.266, A:Y.538, A:Y.544 Water bridges: A:D.38, A:R.430, A:R.543 PEG.40: 10 residues within 4Å: Chain B: L.93, E.94, F.97, P.128, Y.294, Y.299, T.370, I.371, G.372 Ligands: PG4.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.94, B:T.370, B:G.372 PEG.41: 3 residues within 4Å: Chain A: E.478, D.480, R.485 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.478, A:R.485, A:R.485 Water bridges: A:R.477, A:E.478, A:D.480 PEG.42: 5 residues within 4Å: Chain B: F.187, P.188, P.404, E.405 Ligands: PGE.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.405 PEG.43: 7 residues within 4Å: Chain A: R.604 Chain B: L.582, H.584, F.585, R.587, D.590, D.597 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.585, B:R.587, B:D.597, A:R.604, A:R.604 Water bridges: B:F.585 PEG.44: 7 residues within 4Å: Chain A: W.341, G.342 Chain B: W.341, R.362, Y.381, E.391, K.393 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.362, B:R.362, B:Y.381, B:E.389, B:K.393 Water bridges: A:R.359 PEG.45: 8 residues within 4Å: Chain B: D.38, E.245, R.266, Y.538, D.540, R.543, Y.544 Ligands: EDO.32 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.266, B:Y.538, B:Y.538, B:Y.544, B:Y.544 Water bridges: B:E.245, B:R.430, B:R.543

2 x HDZ: NITROGEN MOLECULE(Non-covalent)

HDZ.23: 3 residues within 4Å: Chain A: R.482 Chain B: E.478, A.479 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.482, A:R.482 HDZ.46: 3 residues within 4Å: Chain A: E.478, A.479 Chain B: R.482 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.482, B:R.482

Links

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Citation

Murakawa, T. et al., High-resolution crystal structure of copper amine oxidase from Arthrobacter globiformis: assignment of bound diatomic molecules as O2. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-09-11

Peptides

Phenylethylamine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Phenylethylamine oxidase

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