SMTL ID : 3k5t.1

Crystal structure of human diamine oxidase in space group C2221

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG.1: 6 residues within 4Å: Chain A: L.34, F.83, Q.86, N.90, T.92, F.94 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.34, A:F.83, A:F.94 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.8: 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.9: 5 residues within 4Å: Chain A: P.586, W.589 Chain B: N.518, R.528, V.530 No protein-ligand interaction detected (PLIP)

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

CU.3: 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.10: 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.4: 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.3 CA.5: 4 residues within 4Å: Chain A: E.542, F.633, N.636, E.638 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.542, A:E.542, A:F.633, A:E.638, H2O.9 CA.11: 6 residues within 4Å: Chain B: K.59, D.499, L.500, D.501, D.644, L.645 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.499, B:L.500, B:D.501, B:D.644, B:L.645, H2O.15 CA.12: 4 residues within 4Å: Chain B: E.542, F.633, N.636, E.638 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.542, B:E.542, B:F.633, B:E.638, H2O.20

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: Y.351, D.353, W.356, V.438, Y.439, N.440, Y.441 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.353, A:D.353 Water bridges: A:Y.351, A:Y.351, A:N.440, A:N.440, A:N.440 GOL.13: 7 residues within 4Å: Chain B: Y.351, D.353, W.356, V.438, Y.439, N.440, Y.441 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.353 Water bridges: B:Y.351, B:Y.351, B:Y.351, B:N.440, B:N.440, B:N.440, B:Y.443

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

NAG.7: 4 residues within 4Å: Chain A: N.725, T.727 Chain B: G.702, N.704 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.725, A:T.727 NAG.14: 4 residues within 4Å: Chain A: G.702, N.704 Chain B: N.725, T.727 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.725

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGrath, A.P. et al., A new crystal form of human diamine oxidase. Acta Crystallogr.,Sect.F (2010)

Release Date

2010-02-09

Peptides

Diamine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Diamine oxidase

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