SMTL ID : 2y73.1

THE NATIVE STRUCTURES OF SOLUBLE HUMAN PRIMARY AMINE OXIDASE AOC3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.1: 7 residues within 4Å: Chain A: L.79, F.130, Q.133, N.137, S.139, V.157, P.163 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.79 NAG-NAG-MAN.3: 6 residues within 4Å: Chain B: L.79, F.130, Q.133, N.137, S.139, P.163 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.79

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 8 residues within 4Å: Chain A: R.206, V.209, N.232, S.234 Chain B: Y.448, S.449, H.450, D.728 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.450 NAG-NAG.4: 8 residues within 4Å: Chain A: Y.448, S.449, H.450, D.728 Chain B: R.206, V.209, N.232, S.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.450

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

CU.5: 4 residues within 4Å: Chain A: Y.471, H.520, H.522, H.684 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.520, A:H.522, A:H.684 CU.16: 4 residues within 4Å: Chain B: Y.471, H.520, H.522, H.684 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.520, B:H.522, B:H.684

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: K.106, D.529, L.530, D.531, D.673, L.674 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.529, A:L.530, A:D.531, A:D.673, A:L.674, H2O.2 CA.7: 4 residues within 4Å: Chain A: E.572, F.663, N.665, E.667 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.572, A:F.663, A:E.667, H2O.1, H2O.2 CA.17: 6 residues within 4Å: Chain B: K.106, D.529, L.530, D.531, D.673, L.674 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.529, B:D.531, B:D.673, B:L.674, H2O.9 CA.18: 5 residues within 4Å: Chain B: E.572, K.638, F.663, N.665, E.667 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.572, B:F.663, B:E.667, H2O.8, H2O.8

8 x IMD: IMIDAZOLE(Non-covalent)

IMD.8: 6 residues within 4Å: Chain A: Y.384, D.386, L.468, L.469, N.470, Y.471 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.386 pi-Stacking: A:Y.384 IMD.9: 9 residues within 4Å: Chain A: G.340, P.347, I.349, V.462, R.463, S.464, W.475, T.477 Ligands: IMD.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.477, A:T.477 IMD.10: 7 residues within 4Å: Chain A: P.347, L.365, D.476, T.477, I.487, F.526 Ligands: IMD.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.477 IMD.13: 3 residues within 4Å: Chain A: Y.176, Y.394, L.469 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.394 IMD.19: 9 residues within 4Å: Chain B: G.340, P.347, I.349, V.462, R.463, S.464, W.475, T.477 Ligands: IMD.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.477 IMD.20: 4 residues within 4Å: Chain B: Y.176, T.212, Y.394, L.469 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.212 IMD.21: 6 residues within 4Å: Chain B: Y.384, D.386, L.468, L.469, N.470, Y.471 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:Y.384 IMD.24: 7 residues within 4Å: Chain B: P.347, L.365, D.476, T.477, I.487, F.526 Ligands: IMD.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.347, B:L.365

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.11: 3 residues within 4Å: Chain A: W.538, N.592, H.593 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.592 NAG.12: 1 residues within 4Å: Chain A: N.666 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.666 NAG.22: 2 residues within 4Å: Chain B: N.592, H.593 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.593 NAG.23: 1 residues within 4Å: Chain B: N.666 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.666

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.14: 6 residues within 4Å: Chain A: R.383, L.615, S.619, M.621 Chain B: L.559, Q.560 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.383, A:R.383, B:Q.560 FMT.15: 5 residues within 4Å: Chain A: L.314, Q.315, P.405, Y.406 Chain B: N.435 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.315, A:Y.406, B:N.435 Water bridges: A:L.407

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Elovaara, H. et al., Identification of Two Imidazole Binding Sites and Key Residues for Substrate Specificity in Human Primary Amine Oxidase Aoc3. Biochemistry (2011)

Release Date

2011-06-15

Peptides

MEMBRANE PRIMARY AMINE OXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MEMBRANE PRIMARY AMINE OXIDASE

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