SMTL ID : 4c8r.2 (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 Compare

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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.203, A:D.205, A:H.348 NI.8: 4 residues within 4Å: Chain B: H.203, D.205, H.348 Ligands: 6YT.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.203, B:D.205, B:H.348, H2O.5

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: 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.9: 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: 11 residues within 4Å: Chain A: W.182, V.184, L.200, H.203, D.205, L.218, H.348, R.350, R.361 Ligands: NI.1, EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.182, A:V.184 Salt bridges: A:R.350, A:R.361 6YT.10: 11 residues within 4Å: Chain B: Y.178, W.182, L.200, H.203, D.205, Q.216, L.218, H.348, R.350, R.361 Ligands: NI.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.178, B:W.182 Hydrogen bonds: B:Q.216 Salt bridges: B:R.350, B:R.361

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

EDO.4: 5 residues within 4Å: Chain A: Y.178, Y.206, D.262, N.293 Ligands: 6YT.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.206, A:D.262, A:N.293 Water bridges: A:T.296 EDO.5: 3 residues within 4Å: Chain A: H.210, K.275 Chain B: F.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.210 EDO.6: 6 residues within 4Å: Chain A: Y.116, W.117, G.118, E.120, N.237, K.241 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.120, A:N.237, A:K.241, A:K.241 EDO.7: 2 residues within 4Å: Chain A: A.58, D.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.58

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
C

B
D

GAMMA-BUTYROBETAINE DIOXYGENASE

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