SMTL ID : 6csb.3 (3 other biounits)

V308E mutant of cytochrome P450 2D6 complexed with thioridazine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

monomer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: R.79, V.97, F.98, W.106, R.110, I.164, A.283, G.284, T.287, T.288, T.291, Q.342, V.352, H.354, L.377, P.413, F.414, S.415, R.419, C.421, L.422, G.423, L.426, A.427, E.430 Ligands: 2CV.5 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:V.97, A:F.98, A:F.98, A:I.164, A:V.352, A:L.377, A:F.414, A:F.414, A:L.422, A:L.426 Hydrogen bonds: A:F.98, A:S.415, A:S.415 Water bridges: A:V.352 Salt bridges: A:R.79, A:R.79, A:R.110, A:H.354, A:R.419 Metal complexes: A:C.421

2 x RTZ: 10-{2-[(2R)-1-methylpiperidin-2-yl]ethyl}-2-(methylsulfanyl)-10H-phenothiazine(Non-covalent)

RTZ.2: 14 residues within 4Å: Chain A: L.88, F.90, F.98, L.99, A.187, G.190, L.191, E.194, Q.222, A.278, D.279, S.282 Ligands: RTZ.3, 2CV.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.88, A:F.98, A:F.98, A:L.191, A:E.194, A:A.278 Salt bridges: A:D.279 RTZ.3: 5 residues within 4Å: Chain A: T.32, L.350, G.351, F.459 Ligands: RTZ.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.32, A:L.350, A:F.459

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: R.110, V.114, L.422, E.424, P.425 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.110, A:L.422, A:E.424

1 x 2CV: HEGA-10(Non-covalent)

2CV.5: 7 residues within 4Å: Chain A: F.98, A.283, T.287, V.348, V.352 Ligands: HEM.1, RTZ.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.348

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: C.169, H.236, D.248, E.251 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.236, A:D.248, A:E.251 ZN.7: 1 residues within 4Å: Chain A: C.471 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y.T. et al., Characteristic conformational changes on the distal and proximal surfaces of cytochrome P450 2D6 in response to substrate binding. To Be Published

Release Date

2019-03-27

Peptides

Cytochrome P450 2D6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Cytochrome P450 2D6

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