SMTL ID : 3hig.1

Crystal structure of human diamine oxidase in complex with the inhibitor berenil

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 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

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: L.34, F.83, Q.86, N.90, T.92 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.34, A:F.83

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: 5 residues within 4Å: Chain A: N.518, R.528, V.530 Chain B: P.586, W.589 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.725 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 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.34, B:F.83, B:F.94 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: 4 residues within 4Å: Chain A: G.702, N.704 Chain B: N.725, T.727 No protein-ligand interaction detected (PLIP)

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

CU.7: 4 residues within 4Å: Chain A: Y.441, H.490, H.492, H.655 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.490, A:H.492, A:H.655 CU.12: 4 residues within 4Å: Chain B: Y.441, H.490, H.492, H.655 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.490, B:H.492, B:H.655

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.13: 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.25 CA.14: 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.19, H2O.24

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain A: L.292, E.293, G.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.292, A:G.294

2 x BRN: BERENIL(Non-covalent)

BRN.11: 12 residues within 4Å: Chain A: Y.128, Y.132, F.164, T.165, D.166, Y.351, D.353, W.356, V.438, Y.439, N.440 Chain B: F.415 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.356, A:W.356, A:V.438, A:Y.439, A:Y.439 Hydrogen bonds: A:D.166, A:D.353, A:W.356 Water bridges: A:T.125, A:Y.132, A:Y.132, A:V.438 pi-Stacking: A:Y.128, A:Y.351 BRN.15: 11 residues within 4Å: Chain A: F.415 Chain B: Y.128, F.164, T.165, D.166, Y.351, D.353, W.356, V.438, Y.439, N.440 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.438, B:Y.439, B:Y.439 Hydrogen bonds: B:Y.128, B:D.166, B:D.166, B:D.353, B:W.356 Water bridges: B:T.125, B:Y.443 pi-Stacking: B:Y.128, B:Y.351, B:W.356

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGrath, A.P. et al., Structure and inhibition of human diamine oxidase. Biochemistry (2009)

Release Date

2009-10-20

Peptides

Amiloride-sensitive amine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Amiloride-sensitive amine oxidase

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