SMTL ID : 4qfd.3 (2 other biounits)

Co-crystal structure of compound 2 (3-(7-hydroxy-2-oxo-4-phenyl-2H-chromen-6-yl)propanoic acid) and FAD bound to human DAAO at 2.85A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-tetramer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 4 residues within 4Å: Chain A: L.122, F.125, P.126, Y.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.125 NA.4: 4 residues within 4Å: Chain B: L.122, F.125, P.126, Y.128 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.126 NA.7: 4 residues within 4Å: Chain C: L.122, F.125, P.126, Y.128 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.125 NA.10: 4 residues within 4Å: Chain D: L.122, F.125, P.126, Y.128 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.122

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 35 residues within 4Å: Chain A: I.6, G.7, A.8, G.9, V.10, I.11, A.36, D.37, R.38, T.43, T.44, T.45, V.47, A.48, A.49, G.50, L.51, R.162, V.164, C.181, T.182, G.183, W.185, Y.228, G.281, F.282, R.283, P.284, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 31R.3 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:T.44, A:V.47, A:A.48, A:R.283 Hydrogen bonds: A:A.8, A:G.9, A:I.11, A:D.37, A:D.37, A:R.38, A:R.38, A:T.43, A:T.44, A:T.45, A:T.45, A:A.49, A:G.50, A:L.51, A:L.51, A:V.164, A:V.164, A:G.312, A:G.315, A:L.316, A:T.317 Water bridges: A:G.12, A:G.183 FAD.5: 39 residues within 4Å: Chain B: I.6, G.7, A.8, G.9, V.10, I.11, G.12, A.36, D.37, R.38, T.43, T.44, T.45, V.47, A.48, A.49, G.50, L.51, R.162, K.163, V.164, C.181, T.182, G.183, W.185, I.202, Y.228, G.281, F.282, R.283, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 31R.6 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:V.47, B:I.202, B:R.283 Hydrogen bonds: B:A.8, B:G.9, B:I.11, B:G.12, B:D.37, B:R.38, B:R.38, B:T.44, B:T.44, B:T.45, B:T.45, B:A.49, B:G.50, B:L.51, B:L.51, B:V.164, B:V.164, B:G.312, B:G.315, B:L.316, B:T.317, B:T.317 FAD.8: 35 residues within 4Å: Chain C: I.6, G.7, A.8, G.9, V.10, I.11, A.36, D.37, R.38, T.43, T.44, T.45, V.47, A.48, A.49, G.50, L.51, R.162, V.164, C.181, T.182, G.183, W.185, Y.228, G.281, F.282, R.283, P.284, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 31R.9 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:T.44, C:V.47, C:A.48, C:R.283 Hydrogen bonds: C:A.8, C:G.9, C:I.11, C:D.37, C:R.38, C:R.38, C:T.43, C:T.44, C:T.44, C:T.45, C:A.49, C:G.50, C:L.51, C:L.51, C:V.164, C:V.164, C:G.312, C:G.315, C:L.316, C:T.317, C:T.317 Water bridges: C:G.12, C:G.183, C:H.311 FAD.11: 39 residues within 4Å: Chain D: I.6, G.7, A.8, G.9, V.10, I.11, G.12, A.36, D.37, R.38, T.43, T.44, T.45, V.47, A.48, A.49, G.50, L.51, R.162, K.163, V.164, C.181, T.182, G.183, W.185, I.202, Y.228, G.281, F.282, R.283, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 31R.12 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:V.47, D:I.202, D:R.283 Hydrogen bonds: D:A.8, D:G.9, D:I.11, D:G.12, D:D.37, D:R.38, D:R.38, D:T.44, D:T.45, D:T.45, D:A.49, D:G.50, D:L.51, D:L.51, D:V.164, D:V.164, D:G.312, D:G.315, D:L.316, D:T.317

4 x 31R: 3-(7-hydroxy-2-oxo-4-phenyl-2H-chromen-6-yl)propanoic acid(Non-covalent)

31R.3: 15 residues within 4Å: Chain A: L.51, Q.53, P.54, Y.55, L.56, L.215, T.216, H.217, Y.224, S.226, Y.228, G.240, R.283, G.313 Ligands: FAD.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.215, A:Y.224, A:Y.224, A:Y.228 Hydrogen bonds: A:Q.53, A:L.56, A:Y.228, A:G.313 Salt bridges: A:H.217, A:R.283 pi-Stacking: A:Y.55, A:Y.55, A:Y.228 31R.6: 14 residues within 4Å: Chain B: L.51, Q.53, P.54, Y.55, L.56, T.216, H.217, Y.224, S.226, Y.228, G.240, R.283, G.313 Ligands: FAD.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.55, B:Y.224, B:Y.228 Hydrogen bonds: B:Q.53, B:Y.55, B:L.56, B:Y.228, B:Y.228 Water bridges: B:G.240 Salt bridges: B:H.217, B:R.283 pi-Stacking: B:Y.55, B:Y.55, B:Y.228 31R.9: 15 residues within 4Å: Chain C: L.51, Q.53, P.54, Y.55, L.56, L.215, T.216, H.217, Y.224, S.226, Y.228, G.240, R.283, G.313 Ligands: FAD.8 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.215, C:Y.224, C:Y.224, C:Y.228 Hydrogen bonds: C:Q.53, C:Y.55, C:L.56, C:G.313 Salt bridges: C:H.217, C:R.283 pi-Stacking: C:Y.55, C:Y.55, C:Y.228 31R.12: 14 residues within 4Å: Chain D: L.51, Q.53, P.54, Y.55, L.56, T.216, H.217, Y.224, S.226, Y.228, G.240, R.283, G.313 Ligands: FAD.11 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.55, D:Y.224, D:Y.228 Hydrogen bonds: D:Q.53, D:L.56, D:Y.228 Water bridges: D:G.240 Salt bridges: D:H.217, D:R.283 pi-Stacking: D:Y.55, D:Y.55, D:Y.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Terry-Lorenzo, R.T. et al., Novel human D-amino acid oxidase inhibitors stabilize an active-site lid-open conformation. Biosci.Rep. (2014)

Release Date

2014-07-16

Peptides

D-amino-acid oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

D-amino-acid oxidase

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