SMTL ID : 5vc0.2 (1 other biounit)

Crystal structure of human CYP3A4 bound to ritonavir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 27 residues within 4Å: Chain A: R.85, I.98, S.99, W.106, R.110, I.281, F.282, A.285, T.289, V.293, I.349, A.350, L.353, R.355, P.414, F.415, G.416, S.417, R.420, N.421, C.422, I.423, G.424, F.427, A.428, M.432 Ligands: RIT.2 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:I.98, A:I.281, A:F.282, A:A.285, A:T.289, A:V.293, A:I.349, A:A.350, A:F.415, A:F.415, A:I.423, A:F.427 Hydrogen bonds: A:S.417 Salt bridges: A:R.85, A:R.85, A:R.110, A:R.355, A:R.420 Metal complexes: A:C.422 HEM.3: 27 residues within 4Å: Chain B: R.85, I.98, S.99, W.106, R.110, I.281, F.282, A.285, T.289, V.293, I.349, A.350, L.353, R.355, P.414, F.415, G.416, S.417, R.420, N.421, C.422, I.423, G.424, F.427, A.428, M.432 Ligands: RIT.4 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:I.98, B:I.281, B:F.282, B:A.285, B:T.289, B:V.293, B:I.349, B:A.350, B:F.415, B:F.415, B:I.423, B:F.427 Hydrogen bonds: B:S.417 Salt bridges: B:R.85, B:R.85, B:R.110, B:R.355, B:R.420 Metal complexes: B:C.422 HEM.5: 27 residues within 4Å: Chain C: R.85, I.98, S.99, W.106, R.110, I.281, F.282, A.285, T.289, V.293, I.349, A.350, L.353, R.355, P.414, F.415, G.416, S.417, R.420, N.421, C.422, I.423, G.424, F.427, A.428, M.432 Ligands: RIT.6 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:I.98, C:I.281, C:F.282, C:A.285, C:T.289, C:V.293, C:I.349, C:A.350, C:F.415, C:F.415, C:I.423, C:F.427 Hydrogen bonds: C:S.417 Salt bridges: C:R.85, C:R.85, C:R.110, C:R.355, C:R.420 Metal complexes: C:C.422 HEM.7: 27 residues within 4Å: Chain D: R.85, I.98, S.99, W.106, R.110, I.281, F.282, A.285, T.289, V.293, I.349, A.350, L.353, R.355, P.414, F.415, G.416, S.417, R.420, N.421, C.422, I.423, G.424, F.427, A.428, M.432 Ligands: RIT.8 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:I.98, D:I.281, D:F.282, D:A.285, D:T.289, D:V.293, D:I.349, D:A.350, D:F.415, D:F.415, D:I.423, D:F.427 Hydrogen bonds: D:S.417 Salt bridges: D:R.85, D:R.85, D:R.110, D:R.355, D:R.420 Metal complexes: D:C.422

4 x RIT: RITONAVIR(Non-covalent)

RIT.2: 20 residues within 4Å: Chain A: F.37, D.56, R.85, R.86, F.88, S.99, I.100, L.190, L.191, F.193, F.195, T.204, I.281, F.284, A.285, T.289, I.349, A.350, R.352 Ligands: HEM.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.88, A:F.88, A:L.190, A:L.191, A:T.204, A:I.281, A:F.284, A:F.284, A:I.349, A:A.350 Hydrogen bonds: A:S.99, A:S.99 RIT.4: 20 residues within 4Å: Chain B: F.37, D.56, R.85, R.86, F.88, S.99, I.100, L.190, L.191, F.193, F.195, T.204, I.281, F.284, A.285, T.289, I.349, A.350, R.352 Ligands: HEM.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.88, B:F.88, B:L.190, B:L.191, B:T.204, B:I.281, B:F.284, B:F.284, B:I.349, B:A.350 Hydrogen bonds: B:S.99, B:S.99 RIT.6: 20 residues within 4Å: Chain C: F.37, D.56, R.85, R.86, F.88, S.99, I.100, L.190, L.191, F.193, F.195, T.204, I.281, F.284, A.285, T.289, I.349, A.350, R.352 Ligands: HEM.5 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.88, C:F.88, C:L.190, C:L.191, C:T.204, C:I.281, C:F.284, C:F.284, C:I.349, C:A.350 Hydrogen bonds: C:S.99, C:S.99 RIT.8: 20 residues within 4Å: Chain D: F.37, D.56, R.85, R.86, F.88, S.99, I.100, L.190, L.191, F.193, F.195, T.204, I.281, F.284, A.285, T.289, I.349, A.350, R.352 Ligands: HEM.7 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.88, D:F.88, D:L.190, D:L.191, D:T.204, D:I.281, D:F.284, D:F.284, D:I.349, D:A.350 Hydrogen bonds: D:S.99, D:S.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sevrioukova, I.F., High-Level Production and Properties of the Cysteine-Depleted Cytochrome P450 3A4. Biochemistry (2017)

Release Date

2017-05-31

Peptides

Cytochrome P450 3A4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Cytochrome P450 3A4

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