SMTL ID : 5lth.1

Crystal structure of the alpha subunit of heme dependent oxidative N-demethylase (HODM) in complex with the dimethylamine substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 21 residues within 4Å: Chain A: Y.38, S.39, L.160, W.180, D.185, F.190, W.193, H.194, P.196, V.197, V.205, F.206, A.209, L.213, R.224, N.226, W.227, F.281, Y.317, K.318 Ligands: DMN.2 25 PLIP interactions: 24 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:Y.38, A:L.160, A:W.180, A:W.193, A:V.197, A:V.205, A:F.206, A:F.206, A:L.213, A:L.213, A:F.281, A:F.281, A:F.281, A:Y.317 Hydrogen bonds: A:Y.38, A:N.226, A:Y.317 Water bridges: A:W.227, A:K.318, A:K.318 Salt bridges: A:K.318 pi-Stacking: A:F.190, A:F.281 Metal complexes: A:H.194, H2O.8

1 x DMN: DIMETHYLAMINE(Non-covalent)

DMN.2: 4 residues within 4Å: Chain A: W.180, E.266, Q.268 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.268 Water bridges: A:R.224

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

PEG.3: 4 residues within 4Å: Chain A: E.33, M.37, S.39 Ligands: NA.4 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 1 residues within 4Å: Ligands: PEG.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ortmayer, M. et al., An oxidative N-demethylase reveals PAS transition from ubiquitous sensor to enzyme. Nature (2016)

Release Date

2016-11-09

Peptides

heme dependent oxidative N-demethylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

heme dependent oxidative N-demethylase

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