SMTL ID : 2y74.1

THE CRYSTAL STRUCTURE OF HUMAN SOLUBLE PRIMARY AMINE OXIDASE AOC3 IN THE OFF-COPPER CONFORMATION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-dimer

Ligands

1 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: F.130, Q.133, N.137, S.139, M.152, V.157, P.163 No protein-ligand interaction detected (PLIP)

3 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: 7 residues within 4Å: Chain A: R.206, L.208, V.209, N.232, S.234 Chain B: Y.448, D.728 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain B: L.79, F.130, Q.133, N.137, S.139, P.163 Ligands: MAN.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.79, B:F.130 NAG-NAG.4: 6 residues within 4Å: Chain A: Y.448, S.449, H.450, D.728 Chain B: N.232, S.234 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:H.450 Hydrogen bonds: A:H.450

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

CU.5: 3 residues within 4Å: Chain A: H.520, H.522, H.684 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.520, A:H.522, A:H.684, H2O.1, H2O.3 CU.13: 4 residues within 4Å: Chain B: Y.471, H.520, H.522, H.684 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.520, B:H.522, B:H.684, H2O.3

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: E.572, K.638, F.663, N.665, E.667 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.572, A:E.572, A:F.663, A:E.667, H2O.1 CA.7: 6 residues within 4Å: Chain A: K.106, D.529, L.530, D.531, D.673, L.674 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.529, A:L.530, A:D.673, A:L.674, H2O.1 CA.14: 6 residues within 4Å: Chain B: K.106, D.529, L.530, D.531, D.673, L.674 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.529, B:L.530, B:D.531, B:D.673, B:L.674, H2O.3 CA.15: 4 residues within 4Å: Chain B: E.572, F.663, N.665, E.667 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.572, B:E.572, B:F.663, B:E.667

6 x IMD: IMIDAZOLE(Non-covalent)

IMD.8: 2 residues within 4Å: Chain A: Y.176, Y.394 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.394 pi-Stacking: A:Y.176 IMD.9: 7 residues within 4Å: Chain A: P.347, V.462, R.463, S.464, W.475, T.477 Ligands: IMD.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.464 IMD.10: 8 residues within 4Å: Chain A: P.347, I.363, L.365, D.476, T.477, I.487, F.526 Ligands: IMD.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.365 IMD.16: 3 residues within 4Å: Chain B: Y.176, Y.394, L.469 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.394 IMD.17: 6 residues within 4Å: Chain B: P.347, V.462, S.464, W.475, T.477 Ligands: IMD.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.464, B:T.477 IMD.18: 9 residues within 4Å: Chain B: P.347, S.364, L.365, W.475, D.476, T.477, I.487, F.526 Ligands: IMD.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.365

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

NAG.11: 2 residues within 4Å: Chain A: N.592, H.593 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain A: N.666 No protein-ligand interaction detected (PLIP) NAG.20: 3 residues within 4Å: Chain B: W.538, N.592, H.593 No protein-ligand interaction detected (PLIP) NAG.21: 1 residues within 4Å: Chain B: N.666 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.666

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.19: 1 residues within 4Å: Ligands: NAG-NAG.3 No protein-ligand interaction detected (PLIP)

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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