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

Crystal structure of the cysteine depleted CYP3A4 bound to bromoergocryptine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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, F.117, F.282, A.285, G.286, 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, A.428, M.432 Ligands: 08Y.2 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:I.98, A:F.117, A:A.285, A:V.293, A:I.349, A:A.350, A:L.353, A:F.415, A:F.415, A:I.423 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.7: 27 residues within 4Å: Chain B: R.85, I.98, S.99, W.106, R.110, F.117, F.282, A.285, G.286, 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, A.428, M.432 Ligands: 08Y.8 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:I.98, B:F.117, B:A.285, B:V.293, B:I.349, B:A.350, B:L.353, B:F.415, B:F.415, B:I.423 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.13: 27 residues within 4Å: Chain C: R.85, I.98, S.99, W.106, R.110, F.117, F.282, A.285, G.286, 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, A.428, M.432 Ligands: 08Y.14 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:I.98, C:F.117, C:A.285, C:V.293, C:I.349, C:A.350, C:L.353, C:F.415, C:F.415, C:I.423 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.19: 27 residues within 4Å: Chain D: R.85, I.98, S.99, W.106, R.110, F.117, F.282, A.285, G.286, 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, A.428, M.432 Ligands: 08Y.20 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:I.98, D:F.117, D:A.285, D:V.293, D:I.349, D:A.350, D:L.353, D:F.415, D:F.415, D:I.423 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 08Y: bromoergocryptine(Non-covalent)

08Y.2: 16 residues within 4Å: Chain A: F.37, D.56, R.85, F.88, S.99, I.100, R.192, F.195, T.204, F.284, A.285, T.289, A.350, R.352, E.354 Ligands: HEM.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.37, A:F.88, A:F.88, A:I.100, A:F.195, A:F.195, A:F.195, A:F.195, A:F.284, A:A.285, A:T.289, A:A.350 Hydrogen bonds: A:S.99, A:T.204 Salt bridges: A:R.192, A:E.354 pi-Stacking: A:F.195 pi-Cation interactions: A:R.86 08Y.8: 16 residues within 4Å: Chain B: F.37, D.56, R.85, F.88, S.99, I.100, R.192, F.195, T.204, F.284, A.285, T.289, A.350, R.352, E.354 Ligands: HEM.7 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.37, B:F.88, B:F.88, B:I.100, B:F.195, B:F.195, B:F.195, B:F.195, B:F.284, B:A.285, B:T.289, B:A.350 Hydrogen bonds: B:S.99, B:T.204 Salt bridges: B:R.192, B:E.354 pi-Stacking: B:F.195 pi-Cation interactions: B:R.86 08Y.14: 16 residues within 4Å: Chain C: F.37, D.56, R.85, F.88, S.99, I.100, R.192, F.195, T.204, F.284, A.285, T.289, A.350, R.352, E.354 Ligands: HEM.13 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:F.37, C:F.88, C:F.88, C:I.100, C:F.195, C:F.195, C:F.195, C:F.195, C:F.284, C:A.285, C:T.289, C:A.350 Hydrogen bonds: C:S.99, C:T.204 Salt bridges: C:R.192, C:E.354 pi-Stacking: C:F.195 pi-Cation interactions: C:R.86 08Y.20: 16 residues within 4Å: Chain D: F.37, D.56, R.85, F.88, S.99, I.100, R.192, F.195, T.204, F.284, A.285, T.289, A.350, R.352, E.354 Ligands: HEM.19 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:F.37, D:F.88, D:F.88, D:I.100, D:F.195, D:F.195, D:F.195, D:F.195, D:F.284, D:A.285, D:T.289, D:A.350 Hydrogen bonds: D:S.99, D:T.204 Salt bridges: D:R.192, D:E.354 pi-Stacking: D:F.195 pi-Cation interactions: D:R.86

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: Y.387, W.388, T.389, R.398 Ligands: GOL.5 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: F.13, I.18, P.19, G.20, T.22, Y.55 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: K.386, Y.387, T.389 Ligands: GOL.3 Ligand excluded by PLIP GOL.6: 11 residues within 4Å: Chain A: K.35, G.36, F.37, A.38, M.39, M.351, L.457, S.458, G.460, L.462, L.463 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain B: Y.387, W.388, T.389, R.398 Ligands: GOL.11 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain B: F.13, I.18, P.19, G.20, T.22, Y.55 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain B: K.386, Y.387, T.389 Ligands: GOL.9 Ligand excluded by PLIP GOL.12: 11 residues within 4Å: Chain B: K.35, G.36, F.37, A.38, M.39, M.351, L.457, S.458, G.460, L.462, L.463 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain C: Y.387, W.388, T.389, R.398 Ligands: GOL.17 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain C: F.13, I.18, P.19, G.20, T.22, Y.55 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain C: K.386, Y.387, T.389 Ligands: GOL.15 Ligand excluded by PLIP GOL.18: 11 residues within 4Å: Chain C: K.35, G.36, F.37, A.38, M.39, M.351, L.457, S.458, G.460, L.462, L.463 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain D: Y.387, W.388, T.389, R.398 Ligands: GOL.23 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain D: F.13, I.18, P.19, G.20, T.22, Y.55 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain D: K.386, Y.387, T.389 Ligands: GOL.21 Ligand excluded by PLIP GOL.24: 11 residues within 4Å: Chain D: K.35, G.36, F.37, A.38, M.39, M.351, L.457, S.458, G.460, L.462, L.463 Ligand excluded by PLIP

Links

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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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