SMTL ID : 4c8r.1 (2 other biounits)

Human gamma-butyrobetaine dioxygenase (BBOX1) in complex with Ni(II) and N-(3-hydroxypicolinoyl)-S-(pyridin-2-ylmethyl)-L-cysteine (AR692B)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

homo-dimer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.203, D.205, H.348 Ligands: 6YT.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.203, A:D.205, A:D.205, A:H.348 NI.7: 4 residues within 4Å: Chain B: H.203, D.205, H.348 Ligands: 6YT.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.203, B:D.205, B:H.348

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: R.36, C.39, C.41, C.44, H.83 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.39, A:C.41, A:C.44, A:H.83 ZN.8: 4 residues within 4Å: Chain B: C.39, C.41, C.44, H.83 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.39, B:C.41, B:C.44, B:H.83

2 x 6YT: N-(3-hydroxypicolinoyl)-S-(pyridin-2-ylmethyl)-L-cysteine(Non-covalent)

6YT.3: 12 residues within 4Å: Chain A: L.200, H.203, D.205, L.218, S.230, F.341, H.348, G.349, R.350, R.361 Ligands: NI.1, EDO.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.218, A:F.341, A:H.348 Water bridges: A:N.293 Salt bridges: A:R.350, A:R.361 6YT.9: 14 residues within 4Å: Chain B: V.184, L.200, H.203, D.205, Q.216, L.218, S.230, F.341, H.348, G.349, R.350, R.361 Ligands: NI.7, EDO.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.218, B:F.341, B:H.348 Hydrogen bonds: B:R.350 Salt bridges: B:R.361

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

EDO.4: 2 residues within 4Å: Chain A: H.210 Chain B: F.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.210 EDO.5: 4 residues within 4Å: Chain A: Q.115, L.121, Q.122, P.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.122 EDO.6: 3 residues within 4Å: Chain A: Y.178, W.182 Ligands: 6YT.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.183 EDO.10: 3 residues within 4Å: Chain B: Y.178, W.182 Ligands: 6YT.9 No protein-ligand interaction detected (PLIP) EDO.11: 5 residues within 4Å: Chain B: Y.116, W.117, E.120, N.237, K.241 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.116, B:K.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rydzik, A.M. et al., Modulating carnitine levels by targeting its biosynthesis pathway - selective inhibition of gamma-butyrobetaine hydroxylase. Chem Sci (2014)

Release Date

2014-05-14

Peptides

GAMMA-BUTYROBETAINE DIOXYGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GAMMA-BUTYROBETAINE DIOXYGENASE

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