SMTL ID : 4bg1.1

Three dimensional structure of human gamma-butyrobetaine hydroxylase in complex with 1-(3-Carboxypropyl)-1-methylpyrrolidin-1-ium chloride

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

2 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.1: 11 residues within 4Å: Chain A: V.183, A.193, L.199, H.202, D.204, H.347, R.349, R.360, L.362 Ligands: IVL.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.229 Salt bridges: A:H.202, A:R.349, A:R.360 OGA.8: 11 residues within 4Å: Chain B: V.183, A.193, L.199, H.202, D.204, H.347, R.349, R.360, L.362 Ligands: IVL.9, ZN.10 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.229 Salt bridges: B:H.202, B:R.349, B:R.360

2 x IVL: 1-(3-carboxypropyl)-1-methylpyrrolidin-1-ium(Non-covalent)

IVL.2: 12 residues within 4Å: Chain A: Y.177, W.181, N.191, A.193, Y.194, D.204, Y.205, P.206, N.292, T.295, Y.366 Ligands: OGA.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.181, A:N.191, A:A.193, A:Y.194 Hydrogen bonds: A:N.191, A:Y.205, A:N.292 Salt bridges: A:D.204 pi-Cation interactions: A:Y.177, A:W.181, A:W.181 IVL.9: 12 residues within 4Å: Chain B: Y.177, W.181, N.191, A.193, Y.194, D.204, Y.205, P.206, N.292, T.295, Y.366 Ligands: OGA.8 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.181, B:N.191, B:A.193, B:Y.194 Hydrogen bonds: B:N.191, B:Y.205, B:N.292 Water bridges: B:T.295, B:T.295 Salt bridges: B:D.204 pi-Cation interactions: B:Y.177, B:W.181, B:W.181

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.202, D.204, H.347 Ligands: OGA.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.202, A:D.204, A:H.347 ZN.4: 4 residues within 4Å: Chain A: C.38, C.40, C.43, H.82 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.38, A:C.40, A:C.43, A:H.82 ZN.6: 1 residues within 4Å: Chain A: C.267 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.267 ZN.7: 3 residues within 4Å: Chain A: C.3, K.72, D.89 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.3, A:D.89, A:D.89, H2O.5 ZN.10: 4 residues within 4Å: Chain B: H.202, D.204, H.347 Ligands: OGA.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.202, B:D.204, B:H.347 ZN.11: 4 residues within 4Å: Chain B: C.38, C.40, C.43, H.82 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.38, B:C.40, B:C.43, B:H.82 ZN.13: 1 residues within 4Å: Chain B: C.267 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.267 ZN.14: 3 residues within 4Å: Chain B: C.3, K.72, D.89 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.3, B:D.89, B:D.89, H2O.20

2 x 16D: HEXANE-1,6-DIAMINE(Non-covalent)

16D.5: 3 residues within 4Å: Chain A: I.68, Y.75, Y.83 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.75, A:Y.83 Hydrogen bonds: A:Y.75 16D.12: 3 residues within 4Å: Chain B: I.68, Y.75, Y.83 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.75, B:Y.83 Hydrogen bonds: B:Y.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tars, K. et al., Targeting Carnitine Biosynthesis: Discovery of New Inhibitors Against Gamma-Butyrobetaine Hydroxylase. J.Med.Chem. (2014)

Release Date

2014-03-12

Peptides

GAMMA-BUTYROBETAINE DIOXYGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GAMMA-BUTYROBETAINE DIOXYGENASE

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