SMTL ID : 3wa2.1

High resolution crystal structure of copper amine oxidase from arthrobacter globiformis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.08 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: 1PE.30 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.423, A:H.425, A:H.584, H2O.15, H2O.15 CU.36: 4 residues within 4Å: Chain B: H.423, H.425, H.584 Ligands: 1PE.65 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.423, B:H.425, B:H.584, H2O.49, H2O.50

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

NA.2: 7 residues within 4Å: Chain A: R.41, D.432, M.433, F.438, Y.538, D.573, I.574 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.41, A:I.574, A:I.574 NA.37: 7 residues within 4Å: Chain B: R.41, D.432, M.433, F.438, Y.538, 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

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

EDO.3: 9 residues within 4Å: Chain A: Y.33, G.35, V.36, L.37, R.53, R.543, Y.544 Ligands: EDO.11, PEG.22 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: G.406, G.407, S.408, D.409 Ligand excluded by PLIP EDO.5: 13 residues within 4Å: Chain A: W.341, G.342, I.343, L.344, N.360, D.385, R.604 Chain B: K.393, P.595, V.596, D.597, T.598 Ligands: PEG.56 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: G.455, N.456, E.457 Chain B: P.279, S.280, P.281 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: I.182 Ligands: 1PE.31 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: A.523, R.524, A.527, G.555, G.556, A.557, P.560 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: Q.450, T.451, P.454, G.455, N.456, A.461 Ligands: EDO.47 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: I.354, N.355, Y.356, T.357, R.358, A.619 Chain B: T.197 Ligands: PEG.20 Ligand excluded by PLIP EDO.11: 10 residues within 4Å: Chain A: A.7, Y.33, G.35, V.36, F.52, F.241, D.242, V.243, R.266 Ligands: EDO.3 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain A: D.409 Chain B: V.448, Q.450, S.463, R.464, K.465 Ligands: EDO.44, PEG.50 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: F.403, P.404, E.405, G.406, G.407, Q.413 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: R.109, T.179, R.180, V.181, I.182 Ligands: 1PE.31 Ligand excluded by PLIP EDO.38: 9 residues within 4Å: Chain B: Y.33, G.35, V.36, L.37, R.53, R.543, Y.544 Ligands: EDO.46, PEG.57 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain B: G.406, G.407, S.408, D.409 Ligand excluded by PLIP EDO.40: 13 residues within 4Å: Chain A: K.393, P.595, V.596, D.597, T.598 Chain B: W.341, G.342, I.343, L.344, N.360, D.385, R.604 Ligands: PEG.21 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain A: P.279, S.280, P.281 Chain B: G.455, N.456, E.457 Ligand excluded by PLIP EDO.42: 2 residues within 4Å: Chain B: I.182 Ligands: 1PE.66 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain B: A.523, R.524, A.527, G.555, G.556, A.557, P.560 Ligand excluded by PLIP EDO.44: 7 residues within 4Å: Chain B: Q.450, T.451, P.454, G.455, N.456, A.461 Ligands: EDO.12 Ligand excluded by PLIP EDO.45: 8 residues within 4Å: Chain A: T.197 Chain B: I.354, N.355, Y.356, T.357, R.358, A.619 Ligands: PEG.55 Ligand excluded by PLIP EDO.46: 10 residues within 4Å: Chain B: A.7, Y.33, G.35, V.36, F.52, F.241, D.242, V.243, R.266 Ligands: EDO.38 Ligand excluded by PLIP EDO.47: 8 residues within 4Å: Chain A: V.448, Q.450, S.463, R.464, K.465 Chain B: D.409 Ligands: EDO.9, PEG.15 Ligand excluded by PLIP EDO.48: 6 residues within 4Å: Chain B: F.403, P.404, E.405, G.406, G.407, Q.413 Ligand excluded by PLIP EDO.49: 6 residues within 4Å: Chain B: R.109, T.179, R.180, V.181, I.182 Ligands: 1PE.66 Ligand excluded by PLIP

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

PEG.15: 5 residues within 4Å: Chain A: R.464, K.465, R.466, E.500 Ligands: EDO.47 Ligand excluded by PLIP PEG.16: 7 residues within 4Å: Chain A: R.482 Chain B: E.444, R.477, E.478, A.479, D.480, R.485 Ligand excluded by PLIP PEG.17: 9 residues within 4Å: Chain A: V.186, F.187, P.188, A.402, F.403, P.404, E.405, G.406 Ligands: PGE.26 Ligand excluded by PLIP PEG.18: 13 residues within 4Å: Chain A: F.97, A.127, W.160, T.370, G.372, N.373 Chain B: H.347, S.348, D.349, L.350, W.351 Ligands: PGE.24, PGE.28 Ligand excluded by PLIP PEG.19: 8 residues within 4Å: Chain A: R.5, L.6, A.7, S.8, A.9, E.11, R.50, V.319 Ligand excluded by PLIP PEG.20: 6 residues within 4Å: Chain A: R.358, A.619, N.620 Chain B: E.304, C.307 Ligands: EDO.10 Ligand excluded by PLIP PEG.21: 11 residues within 4Å: Chain A: W.341, R.362, Y.381, Y.383, E.389, E.391, K.393 Chain B: W.341, G.342 Ligands: OXY.33, EDO.40 Ligand excluded by PLIP PEG.22: 10 residues within 4Å: Chain A: D.38, E.245, R.266, R.430, Y.538, D.540, R.543, Y.544 Ligands: EDO.3, PEG.23 Ligand excluded by PLIP PEG.23: 9 residues within 4Å: Chain A: L.37, D.38, P.39, A.40, R.41, Y.538, D.540, R.543 Ligands: PEG.22 Ligand excluded by PLIP PEG.50: 5 residues within 4Å: Chain B: R.464, K.465, R.466, E.500 Ligands: EDO.12 Ligand excluded by PLIP PEG.51: 7 residues within 4Å: Chain A: E.444, R.477, E.478, A.479, D.480, R.485 Chain B: R.482 Ligand excluded by PLIP PEG.52: 9 residues within 4Å: Chain B: V.186, F.187, P.188, A.402, F.403, P.404, E.405, G.406 Ligands: PGE.61 Ligand excluded by PLIP PEG.53: 13 residues within 4Å: Chain A: H.347, S.348, D.349, L.350, W.351 Chain B: F.97, A.127, W.160, T.370, G.372, N.373 Ligands: PGE.59, PGE.63 Ligand excluded by PLIP PEG.54: 8 residues within 4Å: Chain B: R.5, L.6, A.7, S.8, A.9, E.11, R.50, V.319 Ligand excluded by PLIP PEG.55: 6 residues within 4Å: Chain A: E.304, C.307 Chain B: R.358, A.619, N.620 Ligands: EDO.45 Ligand excluded by PLIP PEG.56: 11 residues within 4Å: Chain A: W.341, G.342 Chain B: W.341, R.362, Y.381, Y.383, E.389, E.391, K.393 Ligands: EDO.5, OXY.68 Ligand excluded by PLIP PEG.57: 10 residues within 4Å: Chain B: D.38, E.245, R.266, R.430, Y.538, D.540, R.543, Y.544 Ligands: EDO.38, PEG.58 Ligand excluded by PLIP PEG.58: 9 residues within 4Å: Chain B: L.37, D.38, P.39, A.40, R.41, Y.538, D.540, R.543 Ligands: PEG.57 Ligand excluded by PLIP

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

PGE.24: 16 residues within 4Å: Chain A: V.92, L.93, E.94, E.95, E.96, F.97, P.128, L.145, Y.294, Y.299, T.370, I.371, G.372 Chain B: L.350 Ligands: PEG.18, PGE.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.96, A:G.372 PGE.25: 6 residues within 4Å: Chain A: R.497, L.498, D.610, R.611 Chain B: E.192, P.416 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.497 Water bridges: A:N.496 PGE.26: 6 residues within 4Å: Chain A: T.184, G.185, V.186, F.187, E.405 Ligands: PEG.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.405 Water bridges: A:T.184, A:V.186 PGE.27: 5 residues within 4Å: Chain A: E.200, L.201, G.203, P.204 Chain B: R.611 No protein-ligand interaction detected (PLIP) PGE.28: 15 residues within 4Å: Chain A: F.97, A.127, P.128, L.129, W.160, Y.288, Y.294, I.371, G.372, N.373, Y.374, F.399 Chain B: L.350 Ligands: PEG.18, PGE.24 No protein-ligand interaction detected (PLIP) PGE.59: 16 residues within 4Å: Chain A: L.350 Chain B: V.92, L.93, E.94, E.95, E.96, F.97, P.128, L.145, Y.294, Y.299, T.370, I.371, G.372 Ligands: PEG.53, PGE.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.96, B:G.372 PGE.60: 6 residues within 4Å: Chain A: E.192, P.416 Chain B: R.497, L.498, D.610, R.611 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.497 Water bridges: B:N.496 PGE.61: 6 residues within 4Å: Chain B: T.184, G.185, V.186, F.187, E.405 Ligands: PEG.52 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.405 Water bridges: B:T.184, B:V.186 PGE.62: 5 residues within 4Å: Chain A: R.611 Chain B: E.200, L.201, G.203, P.204 No protein-ligand interaction detected (PLIP) PGE.63: 15 residues within 4Å: Chain A: L.350 Chain B: F.97, A.127, P.128, L.129, W.160, Y.288, Y.294, I.371, G.372, N.373, Y.374, F.399 Ligands: PEG.53, PGE.59 No protein-ligand interaction detected (PLIP)

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

PG4.29: 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:D.120 PG4.64: 3 residues within 4Å: Chain B: N.118, L.119, D.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.120 Water bridges: B:D.120

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

1PE.30: 16 residues within 4Å: Chain A: A.394, T.395, H.425, L.582, H.584, F.585, P.586, R.587, D.590, M.594, P.595, V.596, D.597 Chain B: R.604, E.606 Ligands: CU.1 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.584, A:F.585, A:R.587, A:R.587, A:R.587, B:R.604, B:R.604 Water bridges: B:K.505 1PE.31: 7 residues within 4Å: Chain A: V.181, I.182, D.183, T.184, G.185 Ligands: EDO.7, EDO.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.183 1PE.65: 16 residues within 4Å: Chain A: R.604, E.606 Chain B: A.394, T.395, H.425, L.582, H.584, F.585, P.586, R.587, D.590, M.594, P.595, V.596, D.597 Ligands: CU.36 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.604, A:R.604, B:H.584, B:F.585, B:R.587, B:R.587, B:R.587, B:D.597 Water bridges: A:K.505 1PE.66: 7 residues within 4Å: Chain B: V.181, I.182, D.183, T.184, G.185 Ligands: EDO.42, EDO.49 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.183 Water bridges: B:D.183

8 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.32: 5 residues within 4Å: Chain A: W.110, L.148, A.149, V.164, L.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.149 Water bridges: A:V.164, A:V.164 OXY.33: 7 residues within 4Å: Chain A: E.389, E.391, H.509, T.598, V.599, G.600 Ligands: PEG.21 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.598 Water bridges: A:H.509, A:H.509, A:H.509, A:H.509 OXY.34: 4 residues within 4Å: Chain A: R.482 Chain B: E.478, A.479, D.480 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.482, A:R.482, A:R.482, A:R.482, A:R.482 OXY.35: 3 residues within 4Å: Chain A: T.513, L.514, T.530 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.513 Water bridges: B:R.449, B:R.449, B:R.449, B:R.449 OXY.67: 5 residues within 4Å: Chain B: W.110, L.148, A.149, V.164, L.167 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.149 Water bridges: B:V.164, B:V.164 OXY.68: 7 residues within 4Å: Chain B: E.389, E.391, H.509, T.598, V.599, G.600 Ligands: PEG.56 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.389, B:E.391, B:T.598 Water bridges: B:H.509, B:H.509, B:H.509, B:H.509 OXY.69: 4 residues within 4Å: Chain A: E.478, A.479, D.480 Chain B: R.482 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.482, B:R.482, B:R.482, B:R.482, B:R.482 OXY.70: 3 residues within 4Å: Chain B: T.513, L.514, T.530 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.513 Water bridges: A:R.449, A:R.449, A:R.449, A:R.449

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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
X

B
X

Phenylethylamine oxidase

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