SMTL ID : 6gmb.1

Structure of human hydroxyacid oxidase 1 bound with FMN and glycolate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-tetramer

Ligands

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: L.37, A.38, I.41 Ligand excluded by PLIP EDO.2: 4 residues within 4Å: Chain A: G.284, K.285, V.286, E.287 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: C.7, K.296, E.339 Chain D: N.32, D.33, L.168 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: L.54, R.55 Chain D: S.218, W.219 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain B: L.37, A.38, I.41 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain B: G.284, K.285, V.286, E.287 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain B: C.7, K.296, E.339 Chain C: N.32, D.33, L.168 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain B: L.54, R.55 Chain C: S.218, W.219 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain C: L.37, A.38, I.41 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain C: G.284, K.285, V.286, E.287 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: N.32, D.33, L.168 Chain C: C.7, K.296, E.339 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: S.218, W.219 Chain C: L.54, R.55 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain D: L.37, A.38, I.41 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain D: G.284, K.285, V.286, E.287 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: N.32, D.33, L.168 Chain D: C.7, K.296, E.339 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: S.218, W.219 Chain D: L.54, R.55 Ligand excluded by PLIP

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 6 residues within 4Å: Chain A: E.12, R.28, R.295, R.315, P.316, W.319 5 PLIP interactions: 5 interactions with chain A Water bridges: A:I.8, A:E.12, A:R.28, A:R.295, A:R.315 PG4.10: 6 residues within 4Å: Chain B: E.12, R.28, R.295, R.315, P.316, W.319 5 PLIP interactions: 5 interactions with chain B Water bridges: B:I.8, B:E.12, B:R.28, B:R.295, B:R.315 PG4.17: 6 residues within 4Å: Chain C: E.12, R.28, R.295, R.315, P.316, W.319 5 PLIP interactions: 5 interactions with chain C Water bridges: C:I.8, C:E.12, C:R.28, C:R.295, C:R.315 PG4.24: 6 residues within 4Å: Chain D: E.12, R.28, R.295, R.315, P.316, W.319 5 PLIP interactions: 5 interactions with chain D Water bridges: D:I.8, D:E.12, D:R.28, D:R.295, D:R.315

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.6: 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: GOA.7 25 PLIP interactions: 25 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: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.13: 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: GOA.14 25 PLIP interactions: 25 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: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.20: 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: GOA.21 25 PLIP interactions: 25 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: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.27: 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: GOA.28 25 PLIP interactions: 25 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: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 GOA: GLYCOLIC ACID(Non-covalent)

GOA.7: 8 residues within 4Å: Chain A: Y.26, W.110, Y.132, R.167, L.205, H.260, R.263 Ligands: FMN.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.26, A:Y.26, A:Y.132 Salt bridges: A:R.167, A:H.260, A:R.263 GOA.14: 8 residues within 4Å: Chain B: Y.26, W.110, Y.132, R.167, L.205, H.260, R.263 Ligands: FMN.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.26, B:Y.26, B:Y.132 Salt bridges: B:R.167, B:H.260, B:R.263 GOA.21: 8 residues within 4Å: Chain C: Y.26, W.110, Y.132, R.167, L.205, H.260, R.263 Ligands: FMN.20 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.26, C:Y.26, C:Y.132 Salt bridges: C:R.167, C:H.260, C:R.263 GOA.28: 8 residues within 4Å: Chain D: Y.26, W.110, Y.132, R.167, L.205, H.260, R.263 Ligands: FMN.27 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.26, D:Y.26, D:Y.132 Salt bridges: 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 FMN and glycolate. To Be Published

Release Date

2018-06-13

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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