SMTL ID : 3amo.1

Time-resolved X-ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase from Arthrobacter globiformis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

CU.1: 3 residues within 4Å: Chain A: H.431, H.433, H.592 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.431, A:H.433, A:H.592, H2O.1, H2O.10 CU.51: 3 residues within 4Å: Chain B: H.431, H.433, H.592 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.431, B:H.433, B:H.592, H2O.16, H2O.27

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

NA.2: 6 residues within 4Å: Chain A: R.49, D.440, M.441, F.446, D.581, I.582 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.49, A:D.581, A:I.582, A:I.582 NA.52: 6 residues within 4Å: Chain B: R.49, D.440, M.441, F.446, D.581, I.582 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.49, B:M.441, B:I.582

97 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: W.349, R.370, Y.389, Y.391, E.397, E.399 Ligands: GOL.23 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: E.102, F.105, Y.307, T.378, I.379, G.380 Chain B: L.358 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: R.49, R.545, Y.546, D.581 Ligand excluded by PLIP GOL.6: 10 residues within 4Å: Chain A: A.15, L.42, G.43, V.44, F.249, D.250, V.251, V.327, I.328 Ligands: GOL.9 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: L.127, V.159, D.161, H.170, V.197, A.199 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: P.11, L.45, P.47, D.57, R.58, R.59 Ligand excluded by PLIP GOL.9: 11 residues within 4Å: Chain A: G.43, V.44, D.46, G.248, F.249, D.250, V.256, H.258, R.274 Ligands: GOL.6, GOL.15 Ligand excluded by PLIP GOL.10: 10 residues within 4Å: Chain A: E.164, D.165, S.166, N.203, Y.204, T.205 Chain B: D.357, S.360, I.362 Ligands: GOL.39 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: R.457, Q.458, T.459 Chain B: D.525, P.526 Ligand excluded by PLIP GOL.12: 10 residues within 4Å: Chain A: I.39, A.40, Y.41, L.42, V.251, Q.306, I.328, S.329, D.330, A.331 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain A: E.486, A.487, T.521, T.538, K.539, D.540 Chain B: R.490 Ligands: GOL.18 Ligand excluded by PLIP GOL.14: 8 residues within 4Å: Chain A: D.286, P.287, S.288, P.412, S.416, D.417, N.418, I.419 Ligand excluded by PLIP GOL.15: 9 residues within 4Å: Chain A: Y.41, V.44, L.45, D.46, R.61, R.551, Y.552 Ligands: GOL.9, GOL.19 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain A: D.264, F.617, D.618, R.619 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain A: L.506 Chain B: Q.421, P.424, G.425 Ligands: GOL.84 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain A: P.520, T.521, L.522, T.538 Chain B: R.457, R.490 Ligands: GOL.13 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain A: D.46, R.274, R.438, D.548, R.551 Ligands: GOL.15 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain A: K.513, H.515, R.612, E.614 Chain B: T.591, H.592, F.593 Ligand excluded by PLIP GOL.21: 8 residues within 4Å: Chain A: Q.519, T.591, F.593 Chain B: E.453, G.492, K.513, H.515 Ligands: GOL.74 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain A: D.348, R.369 Chain B: P.219, I.220, L.318 Ligand excluded by PLIP GOL.23: 11 residues within 4Å: Chain A: E.347, W.349, R.370, K.401 Chain B: D.348, W.349, G.350 Ligands: GOL.3, GOL.26, GOL.38, GOL.96 Ligand excluded by PLIP GOL.24: 8 residues within 4Å: Chain A: N.363, Y.364, T.365, R.366 Chain B: E.312, C.315, D.316 Ligands: GOL.35 Ligand excluded by PLIP GOL.25: 3 residues within 4Å: Chain A: P.335, R.336, E.337 Ligand excluded by PLIP GOL.26: 7 residues within 4Å: Chain A: I.222, L.318, H.345, E.347 Chain B: D.348 Ligands: GOL.23, GOL.38 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain A: R.457 Chain B: P.526, K.539 Ligands: GOL.92 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain A: G.492, R.493, T.494, H.515, A.516, N.518 Chain B: Q.519 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain A: P.228, F.230, T.231, V.232, T.322 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain A: R.449, E.451, R.474, I.496, S.498, E.508, P.509, E.614 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain A: T.216, K.218 Chain B: P.228, S.229, T.231 Ligands: GOL.77 Ligand excluded by PLIP GOL.32: 2 residues within 4Å: Chain A: S.86, A.87 Ligand excluded by PLIP GOL.33: 3 residues within 4Å: Chain A: D.605, T.606 Chain B: K.610 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain A: R.457, R.490 Chain B: P.520, T.521, L.522 Ligands: GOL.71 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain A: I.362, N.363, R.366 Chain B: T.205 Ligands: GOL.24 Ligand excluded by PLIP GOL.36: 6 residues within 4Å: Chain A: L.111, T.114, D.115, K.184, E.185, V.186 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain A: F.12, P.47, N.259, N.273 Ligand excluded by PLIP GOL.38: 10 residues within 4Å: Chain A: D.316, C.317, L.318, H.345, V.372, Y.387 Chain B: G.350, R.367 Ligands: GOL.23, GOL.26 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain A: F.162, E.164, T.205, D.206 Chain B: I.362 Ligands: GOL.10 Ligand excluded by PLIP GOL.40: 6 residues within 4Å: Chain A: T.29, A.30, G.82, T.83, V.84 Ligands: GOL.49 Ligand excluded by PLIP GOL.41: 5 residues within 4Å: Chain A: H.561, G.563, G.564, A.565, S.569 Ligand excluded by PLIP GOL.42: 5 residues within 4Å: Chain A: P.196, P.198, A.199, P.424, G.425 Ligand excluded by PLIP GOL.43: 6 residues within 4Å: Chain A: Q.421, P.424 Chain B: R.505, L.506 Ligands: GOL.48, GOL.76 Ligand excluded by PLIP GOL.44: 3 residues within 4Å: Chain A: A.123, N.126, D.128 Ligand excluded by PLIP GOL.45: 6 residues within 4Å: Chain A: L.27, R.28, G.31, L.32, L.33, G.34 Ligand excluded by PLIP GOL.46: 1 residues within 4Å: Chain A: S.481 Ligand excluded by PLIP GOL.47: 7 residues within 4Å: Chain A: N.368, Y.391, D.393, T.395, R.612 Chain B: V.604 Ligands: GOL.80 Ligand excluded by PLIP GOL.48: 8 residues within 4Å: Chain A: F.411, P.412, E.413, G.414, G.415, Q.421, G.425 Ligands: GOL.43 Ligand excluded by PLIP GOL.49: 4 residues within 4Å: Chain A: N.81, G.82, T.83 Ligands: GOL.40 Ligand excluded by PLIP GOL.50: 7 residues within 4Å: Chain A: H.65, D.66, A.70, P.72, T.92, E.97, R.151 Ligand excluded by PLIP GOL.53: 8 residues within 4Å: Chain B: G.69, G.149, R.150, R.151, D.180, V.182, S.183 Ligands: GOL.65 Ligand excluded by PLIP GOL.54: 10 residues within 4Å: Chain B: A.15, L.42, G.43, V.44, F.249, D.250, V.251, V.327, I.328 Ligands: GOL.56 Ligand excluded by PLIP GOL.55: 10 residues within 4Å: Chain B: R.532, R.533, T.554, F.557, V.558, H.561, S.562, G.563, G.564, A.565 Ligand excluded by PLIP GOL.56: 11 residues within 4Å: Chain B: G.43, V.44, D.46, G.248, F.249, D.250, V.256, H.258, R.274 Ligands: GOL.54, GOL.66 Ligand excluded by PLIP GOL.57: 4 residues within 4Å: Chain B: L.14, A.15, S.16, S.325 Ligand excluded by PLIP GOL.58: 7 residues within 4Å: Chain B: P.11, V.44, L.45, P.47, D.57, R.58, R.59 Ligand excluded by PLIP GOL.59: 10 residues within 4Å: Chain A: W.349 Chain B: W.349, R.370, Y.389, Y.391, E.397, E.399 Ligands: GOL.73, GOL.80, GOL.83 Ligand excluded by PLIP GOL.60: 7 residues within 4Å: Chain A: L.358 Chain B: F.105, Y.307, T.378, I.379, G.380 Ligands: GOL.70 Ligand excluded by PLIP GOL.61: 6 residues within 4Å: Chain B: V.67, L.101, E.103, V.107, V.181, K.184 Ligand excluded by PLIP GOL.62: 6 residues within 4Å: Chain B: I.26, T.29, A.30, G.82, T.83, V.84 Ligand excluded by PLIP GOL.63: 8 residues within 4Å: Chain B: D.286, S.288, P.412, G.415, S.416, D.417, N.418, I.419 Ligand excluded by PLIP GOL.64: 6 residues within 4Å: Chain B: R.28, L.33, G.34, K.37, A.331, F.332 Ligand excluded by PLIP GOL.65: 8 residues within 4Å: Chain B: H.65, D.66, A.70, P.72, T.92, E.97, R.151 Ligands: GOL.53 Ligand excluded by PLIP GOL.66: 10 residues within 4Å: Chain B: Y.41, V.44, L.45, D.46, R.61, R.551, Y.552 Ligands: GOL.56, GOL.68, GOL.98 Ligand excluded by PLIP GOL.67: 6 residues within 4Å: Chain B: D.264, F.617, D.618, R.619, S.620, P.621 Ligand excluded by PLIP GOL.68: 10 residues within 4Å: Chain B: D.46, R.274, R.438, Y.546, A.547, D.548, E.550, R.551 Ligands: GOL.66, GOL.98 Ligand excluded by PLIP GOL.69: 6 residues within 4Å: Chain B: L.111, T.114, D.115, K.184, E.185, V.186 Ligand excluded by PLIP GOL.70: 5 residues within 4Å: Chain A: S.356 Chain B: Y.307, A.308, N.309 Ligands: GOL.60 Ligand excluded by PLIP GOL.71: 7 residues within 4Å: Chain A: R.490 Chain B: E.486, A.487, T.521, T.538, D.540 Ligands: GOL.34 Ligand excluded by PLIP GOL.72: 6 residues within 4Å: Chain A: E.508 Chain B: F.411, S.416, I.419, S.420, Q.421 Ligand excluded by PLIP GOL.73: 9 residues within 4Å: Chain A: W.349, G.350 Chain B: E.347, W.349, R.370, K.401 Ligands: GOL.59, GOL.78, GOL.80 Ligand excluded by PLIP GOL.74: 11 residues within 4Å: Chain A: N.518, Q.519, P.520 Chain B: A.489, G.492, R.493, T.494, H.515, A.516, N.518 Ligands: GOL.21 Ligand excluded by PLIP GOL.75: 7 residues within 4Å: Chain B: A.93, V.141, E.147, R.148, G.149, R.150, Q.560 Ligand excluded by PLIP GOL.76: 2 residues within 4Å: Chain B: R.505 Ligands: GOL.43 Ligand excluded by PLIP GOL.77: 6 residues within 4Å: Chain B: P.228, F.230, T.231, V.232, T.322 Ligands: GOL.31 Ligand excluded by PLIP GOL.78: 7 residues within 4Å: Chain A: D.348, R.367 Chain B: I.222, L.318, H.345, E.347 Ligands: GOL.73 Ligand excluded by PLIP GOL.79: 4 residues within 4Å: Chain A: D.417, F.430 Chain B: S.471, R.472 Ligand excluded by PLIP GOL.80: 10 residues within 4Å: Chain A: W.349, G.350, I.351 Chain B: E.399, K.401, V.604, T.606 Ligands: GOL.47, GOL.59, GOL.73 Ligand excluded by PLIP GOL.81: 4 residues within 4Å: Chain B: A.123, N.126, L.127, D.128 Ligand excluded by PLIP GOL.82: 7 residues within 4Å: Chain B: R.449, E.451, R.474, I.496, E.508, P.509, E.614 Ligand excluded by PLIP GOL.83: 7 residues within 4Å: Chain A: T.606 Chain B: W.349, Y.391, E.397, K.610 Ligands: GOL.59, GOL.96 Ligand excluded by PLIP GOL.84: 6 residues within 4Å: Chain B: F.411, P.412, E.413, G.414, Q.421 Ligands: GOL.17 Ligand excluded by PLIP GOL.85: 5 residues within 4Å: Chain B: R.267, R.269, D.444, S.502, K.503 Ligand excluded by PLIP GOL.86: 5 residues within 4Å: Chain A: K.610 Chain B: H.517, Q.519, T.606, V.607 Ligand excluded by PLIP GOL.87: 6 residues within 4Å: Chain B: V.159, D.161, H.170, V.197, A.199 Ligands: GOL.89 Ligand excluded by PLIP GOL.88: 3 residues within 4Å: Chain B: A.17, P.335, E.337 Ligand excluded by PLIP GOL.89: 6 residues within 4Å: Chain B: N.126, L.127, D.128, K.131, D.161 Ligands: GOL.87 Ligand excluded by PLIP GOL.90: 5 residues within 4Å: Chain B: L.313, G.319, D.320, I.321 Ligands: GOL.93 Ligand excluded by PLIP GOL.91: 3 residues within 4Å: Chain A: S.471, R.472 Chain B: D.417 Ligand excluded by PLIP GOL.92: 6 residues within 4Å: Chain B: P.526, A.531, A.535, T.538 Ligands: GOL.27, GOL.100 Ligand excluded by PLIP GOL.93: 5 residues within 4Å: Chain B: Q.224, P.225, G.227, D.320 Ligands: GOL.90 Ligand excluded by PLIP GOL.94: 6 residues within 4Å: Chain A: I.362 Chain B: F.162, E.164, N.203, T.205, D.206 Ligand excluded by PLIP GOL.95: 4 residues within 4Å: Chain A: D.525 Chain B: R.457, Q.458, T.459 Ligand excluded by PLIP GOL.96: 8 residues within 4Å: Chain A: K.401, V.604, T.606 Chain B: W.349, I.351, N.368 Ligands: GOL.23, GOL.83 Ligand excluded by PLIP GOL.97: 4 residues within 4Å: Chain B: A.9, P.11, G.52, E.56 Ligand excluded by PLIP GOL.98: 7 residues within 4Å: Chain B: L.45, D.46, P.47, D.548, R.551 Ligands: GOL.66, GOL.68 Ligand excluded by PLIP GOL.99: 4 residues within 4Å: Chain B: R.49, G.50, F.446, D.581 Ligand excluded by PLIP GOL.100: 5 residues within 4Å: Chain B: T.538, K.539, W.542, P.568 Ligands: GOL.92 Ligand excluded by PLIP GOL.101: 3 residues within 4Å: Chain B: R.474, T.475, V.476 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kataoka, M. et al., Detection of the reaction intermediates catalyzed by a copper amine oxidase. J.SYNCHROTRON RADIAT. (2011)

Release Date

2011-11-23

Peptides

Phenylethylamine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phenylethylamine oxidase

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