SMTL ID : 4cwd.1

CRYSTAL STRUCTURE OF HUMAN GAMMA-BUTYROBETAINE,2-OXOGLUTARATE IN COMPLEX WITH 449, A NOVEL SUBSTRATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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: OGA.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.203, A:D.205, A:H.348, H2O.11 NI.6: 4 residues within 4Å: Chain B: H.203, D.205, H.348 Ligands: OGA.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.203, B:D.205, B:H.348, H2O.27

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.7: 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 449: 4-carboxy-1,1-dimethylpiperidin-1-ium(Non-covalent)

449.3: 11 residues within 4Å: Chain A: Y.178, W.182, N.192, Y.195, D.205, Y.206, P.207, N.293, T.296, Y.367 Ligands: OGA.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.178 Hydrogen bonds: A:N.192, A:Y.206, A:N.293 Salt bridges: A:D.205 pi-Cation interactions: A:Y.178, A:W.182 449.8: 11 residues within 4Å: Chain B: Y.178, W.182, N.192, Y.195, D.205, Y.206, P.207, N.293, T.296, Y.367 Ligands: OGA.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.178 Hydrogen bonds: B:N.192, B:Y.206, B:N.293 Water bridges: B:T.296, B:T.296 Salt bridges: B:D.205 pi-Cation interactions: B:Y.178, B:W.182

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

OGA.4: 11 residues within 4Å: Chain A: V.184, A.194, L.200, H.203, D.205, H.348, R.350, R.361, L.363 Ligands: NI.1, 449.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.350 Water bridges: A:Q.216 Salt bridges: A:H.203, A:R.350, A:R.361 OGA.9: 11 residues within 4Å: Chain B: V.184, A.194, L.200, H.203, D.205, H.348, R.350, R.361, L.363 Ligands: NI.6, 449.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.350 Water bridges: B:Q.216 Salt bridges: B:H.203, B:R.350, B:R.361

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 3 residues within 4Å: Chain A: D.71, Y.76, Y.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.71, A:Y.76 PEG.10: 3 residues within 4Å: Chain B: D.71, Y.76, Y.84 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rydzik, A.M. et al., Oxygenase-catalyzed desymmetrization of N,N-dialkyl-piperidine-4-carboxylic acids. Angew. Chem. Int. Ed. Engl. (2014)

Release Date

2014-09-17

Peptides

GAMMA-BUTYROBETAINE DIOXYGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GAMMA-BUTYROBETAINE DIOXYGENASE

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