SMTL ID : 7r4p.1

Structure of human hydroxyacid oxidase 1 bound with 6-amino-1-benzyl-5-(methylamino)pyrimidine-2,4(1H,3H)-dione

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-tetramer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 23 residues within 4Å: Chain A: Y.26, Y.27, A.79, T.80, A.81, S.108, W.110, Q.130, Y.132, T.158, K.236, S.258, H.260, G.261, R.263, D.291, G.292, G.293, R.295, V.313, G.314, R.315 Ligands: I2Z.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.26, A:Y.27, A:T.80, A:R.315 Hydrogen bonds: A:A.79, A:A.81, A:Q.130, A:Q.130, A:K.236, A:K.236, A:S.258, A:G.261, A:G.292, A:G.293, A:G.314, A:R.315 Water bridges: A:H.260, A:H.260, A:D.291, A:D.291, A:V.294, A:V.294, A:R.315, A:R.315 Salt bridges: A:R.295, A:R.315 FMN.3: 23 residues within 4Å: Chain B: Y.26, Y.27, A.79, T.80, A.81, S.108, W.110, Q.130, Y.132, T.158, K.236, S.258, H.260, G.261, R.263, D.291, G.292, G.293, R.295, V.313, G.314, R.315 Ligands: I2Z.4 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:Y.26, B:Y.27, B:T.80, B:R.315 Hydrogen bonds: B:A.79, B:A.81, B:Q.130, B:Q.130, B:K.236, B:K.236, B:S.258, B:G.261, B:G.292, B:G.293, B:G.314, B:R.315 Water bridges: B:H.260, B:H.260, B:D.291, B:D.291, B:V.294, B:V.294, B:R.315, B:R.315 Salt bridges: B:R.295, B:R.315 FMN.5: 23 residues within 4Å: Chain C: Y.26, Y.27, A.79, T.80, A.81, S.108, W.110, Q.130, Y.132, T.158, K.236, S.258, H.260, G.261, R.263, D.291, G.292, G.293, R.295, V.313, G.314, R.315 Ligands: I2Z.6 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:Y.26, C:Y.27, C:T.80, C:R.315 Hydrogen bonds: C:A.79, C:A.81, C:Q.130, C:Q.130, C:K.236, C:K.236, C:S.258, C:G.261, C:G.292, C:G.293, C:G.314, C:R.315 Water bridges: C:H.260, C:H.260, C:D.291, C:D.291, C:V.294, C:V.294, C:R.315, C:R.315 Salt bridges: C:R.295, C:R.315 FMN.7: 23 residues within 4Å: Chain D: Y.26, Y.27, A.79, T.80, A.81, S.108, W.110, Q.130, Y.132, T.158, K.236, S.258, H.260, G.261, R.263, D.291, G.292, G.293, R.295, V.313, G.314, R.315 Ligands: I2Z.8 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:Y.26, D:Y.27, D:T.80, D:R.315 Hydrogen bonds: D:A.79, D:A.81, D:Q.130, D:Q.130, D:K.236, D:K.236, D:S.258, D:G.261, D:G.292, D:G.293, D:G.314, D:R.315 Water bridges: D:H.260, D:H.260, D:D.291, D:D.291, D:V.294, D:V.294, D:R.315, D:R.315 Salt bridges: D:R.295, D:R.315

4 x I2Z: 6-amino-1-benzyl-5-(methylamino)pyrimidine-2,4(1H,3H)-dione(Covalent)

I2Z.2: 10 residues within 4Å: Chain A: Y.26, A.81, M.82, W.110, Y.132, R.167, L.205, H.260, R.263 Ligands: FMN.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.205 Hydrogen bonds: A:Y.26, A:Y.26, A:R.167, A:H.260, A:R.263 I2Z.4: 10 residues within 4Å: Chain B: Y.26, A.81, M.82, W.110, Y.132, R.167, L.205, H.260, R.263 Ligands: FMN.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.205 Hydrogen bonds: B:Y.26, B:Y.26, B:R.167, B:H.260, B:R.263 I2Z.6: 10 residues within 4Å: Chain C: Y.26, A.81, M.82, W.110, Y.132, R.167, L.205, H.260, R.263 Ligands: FMN.5 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.205 Hydrogen bonds: C:Y.26, C:Y.26, C:R.167, C:H.260, C:R.263 I2Z.8: 10 residues within 4Å: Chain D: Y.26, A.81, M.82, W.110, Y.132, R.167, L.205, H.260, R.263 Ligands: FMN.7 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.205 Hydrogen bonds: D:Y.26, D:Y.26, D:R.167, D:H.260, D:R.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mackinnon, S. et al., Structure of human hydroxyacid oxidase 1 bound with 5-bromo-N-methyl-1H-indazole-3-carboxamide. To Be Published

Release Date

2022-05-04

Peptides

Hydroxyacid oxidase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Hydroxyacid oxidase 1

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