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

Crystal structure of the cysteine depleted CYP3A4 bound to bromoergocryptine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 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

2 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

8 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.389, A:T.389, A:R.398 Water bridges: A:Y.387, A:N.406 GOL.4: 6 residues within 4Å: Chain A: F.13, I.18, P.19, G.20, T.22, Y.55 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.18, A:T.22 Water bridges: A:Y.55 GOL.5: 4 residues within 4Å: Chain A: K.386, Y.387, T.389 Ligands: GOL.3 No protein-ligand interaction detected (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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.36, A:F.37, A:A.38, A:M.39 GOL.9: 5 residues within 4Å: Chain B: Y.387, W.388, T.389, R.398 Ligands: GOL.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.389, B:T.389, B:R.398 Water bridges: B:Y.387, B:N.406 GOL.10: 6 residues within 4Å: Chain B: F.13, I.18, P.19, G.20, T.22, Y.55 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.18, B:T.22 Water bridges: B:Y.55 GOL.11: 4 residues within 4Å: Chain B: K.386, Y.387, T.389 Ligands: GOL.9 No protein-ligand interaction detected (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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.36, B:F.37, B:A.38, B:M.39

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome P450 3A4

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