SMTL ID : 3mph.1

The structure of human diamine oxidase complexed with an inhibitor aminoguanidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: L.34, F.83, Q.86, N.90, T.92 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.34

5 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: 4 residues within 4Å: Chain A: N.518, R.528 Chain B: P.586, W.589 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.725, T.727 Chain B: N.704 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain B: L.34, F.83, Q.86, N.90, T.92, F.94 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.34, B:F.83 NAG-NAG.5: 4 residues within 4Å: Chain A: P.586, W.589 Chain B: N.518, R.528 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.704 Chain B: N.725, T.727 No protein-ligand interaction detected (PLIP)

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

CU.7: 3 residues within 4Å: Chain A: H.490, H.492, H.655 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.490, A:H.492, A:H.655, H2O.10 CU.10: 3 residues within 4Å: Chain B: H.490, H.492, H.655 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.490, B:H.492, B:H.655, H2O.30

4 x CA: CALCIUM ION(Non-covalent)

CA.8: 6 residues within 4Å: Chain A: K.59, D.499, L.500, D.501, D.644, L.645 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.499, A:L.500, A:D.501, A:D.644, A:L.645, H2O.1 CA.9: 5 residues within 4Å: Chain A: E.542, R.608, F.633, N.636, E.638 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.542, A:F.633, A:E.638, H2O.1, H2O.3 CA.11: 6 residues within 4Å: Chain B: K.59, D.499, L.500, D.501, D.644, L.645 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.499, B:D.501, B:D.644, B:L.645, H2O.26 CA.12: 4 residues within 4Å: Chain B: E.542, F.633, N.636, E.638 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.542, B:F.633, B:E.638, H2O.20, H2O.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGrath, A.P. et al., Correlation of active site metal content in human diamine oxidase with trihydroxyphenylalanine quinone cofactor biogenesis. Biochemistry (2010)

Release Date

2010-09-08

Peptides

Amiloride-sensitive amine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Amiloride-sensitive amine oxidase