SMTL ID : 2bdm.2 (2 other biounits)

Structure of Cytochrome P450 2B4 with Bound Bifonazole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 20 residues within 4Å: Chain A: G.280, T.283, T.284, T.287, Q.338, V.348, H.350, L.373, P.409, F.410, S.411, R.415, C.417, L.418, G.419, I.422, A.423 Chain B: F.201 Ligands: TMI.2, CM5.5 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:V.348, A:L.373, A:F.410, A:F.410, A:L.418, A:I.422, A:A.423, B:F.201 Hydrogen bonds: A:S.411, A:S.411 Water bridges: A:R.415 Salt bridges: A:H.350, A:R.415 Metal complexes: A:C.417 HEM.9: 20 residues within 4Å: Chain A: F.201 Chain B: G.280, T.283, T.284, T.287, Q.338, V.348, H.350, L.373, P.409, F.410, S.411, R.415, C.417, L.418, G.419, I.422, A.423 Ligands: TMI.10, CM5.13 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:V.348, B:L.373, B:F.410, B:F.410, B:L.418, B:I.422, B:A.423, A:F.201 Hydrogen bonds: B:S.411, B:S.411 Water bridges: B:R.415 Salt bridges: B:H.350, B:R.415 Metal complexes: B:C.417

6 x TMI: 1-[PHENYL-(4-PHENYLPHENYL)-METHYL]IMIDAZOLE(Non-covalent)

TMI.2: 14 residues within 4Å: Chain A: S.109, M.113, L.276, F.277, A.279, G.280, T.283, I.344 Chain B: S.194, V.197, F.198, F.201 Ligands: HEM.1, CM5.5 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.197, B:F.198, A:L.276, A:L.276, A:T.283 pi-Stacking: B:F.198, B:F.201, A:F.277 TMI.3: 16 residues within 4Å: Chain A: F.165, L.179, L.182, F.183, L.219, I.222, I.226, N.268, L.271, T.272, L.274, S.275, F.278 Chain B: P.87, I.88, F.193 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.165, A:L.179, A:L.179, A:L.182, A:L.182, A:F.183, A:L.219, A:I.222, A:I.226, A:L.271, A:L.271, A:L.274, A:F.278, B:P.87, B:F.193, B:F.193 Hydrogen bonds: A:N.268 pi-Stacking: A:F.183 TMI.4: 16 residues within 4Å: Chain A: Q.26, M.27, D.28, R.29, L.32, V.49, Y.50, L.51, V.85, F.346, G.457, V.458 Chain B: E.199, F.204, K.206 Ligands: CM5.8 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.29, A:L.32, A:L.32, A:V.49, A:L.51, A:F.346, A:V.458, B:F.204 pi-Stacking: B:F.204 TMI.10: 14 residues within 4Å: Chain A: S.194, V.197, F.198, F.201 Chain B: S.109, M.113, L.276, F.277, A.279, G.280, T.283, I.344 Ligands: HEM.9, CM5.13 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.276, B:L.276, B:T.283, A:V.197, A:F.198 pi-Stacking: B:F.277, A:F.198, A:F.201 TMI.11: 16 residues within 4Å: Chain A: P.87, I.88, F.193 Chain B: F.165, L.179, L.182, F.183, L.219, I.222, I.226, N.268, L.271, T.272, L.274, S.275, F.278 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.165, B:L.179, B:L.179, B:L.182, B:L.182, B:F.183, B:L.219, B:I.222, B:I.226, B:L.271, B:L.271, B:L.274, B:F.278, A:P.87, A:F.193, A:F.193 Hydrogen bonds: B:N.268 pi-Stacking: B:F.183 TMI.12: 16 residues within 4Å: Chain A: E.199, F.204, K.206 Chain B: Q.26, M.27, D.28, R.29, L.32, V.49, Y.50, L.51, V.85, F.346, G.457, V.458 Ligands: CM5.16 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.29, B:L.32, B:L.32, B:V.49, B:L.51, B:F.346, B:V.458, A:F.204 pi-Stacking: A:F.204

8 x CM5: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE(Non-covalent)

CM5.5: 11 residues within 4Å: Chain A: R.106, S.109, L.110, K.414, R.415, L.418 Chain B: F.89, L.200, F.201 Ligands: HEM.1, TMI.2 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.106, A:K.414, A:R.415 Salt bridges: A:R.106, A:R.106 Hydrophobic interactions: B:F.89, B:L.200 CM5.6: 12 residues within 4Å: Chain A: R.79, I.82, V.94, I.95, F.96, G.99, W.102, R.103, L.205, Y.207 Chain B: V.84, F.89 13 PLIP interactions: 2 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:V.84, B:F.89, A:I.82, A:F.96, A:F.96, A:W.102, A:L.205, A:Y.207 Hydrogen bonds: A:F.96, A:F.96, A:G.99, A:R.103 Water bridges: A:K.81 CM5.7: 14 residues within 4Å: Chain A: V.164, I.226, V.230, E.231, R.234, F.245, I.246, Y.249, E.263, Q.267, L.271, L.274 Chain B: V.20, L.21 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.164, A:I.226, A:F.245, A:I.246, A:Y.249, A:Y.249, A:Q.267, A:L.271, A:L.274, B:V.20, B:L.21 Hydrogen bonds: A:E.231, A:R.234, A:R.234, A:Y.249 Salt bridges: A:R.234 CM5.8: 9 residues within 4Å: Chain A: P.15, S.16, L.18, L.32, S.35, R.38, L.39, F.346 Ligands: TMI.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.32, A:F.346 Hydrogen bonds: A:S.16, A:L.18, A:S.35 Salt bridges: A:R.38 CM5.13: 11 residues within 4Å: Chain A: F.89, L.200, F.201 Chain B: R.106, S.109, L.110, K.414, R.415, L.418 Ligands: HEM.9, TMI.10 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.106, B:K.414, B:R.415 Salt bridges: B:R.106, B:R.106 Hydrophobic interactions: A:F.89, A:L.200 CM5.14: 12 residues within 4Å: Chain A: V.84, F.89 Chain B: R.79, I.82, V.94, I.95, F.96, G.99, W.102, R.103, L.205, Y.207 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.82, B:F.96, B:F.96, B:W.102, B:L.205, B:Y.207, A:V.84, A:F.89 Hydrogen bonds: B:F.96, B:F.96, B:G.99, B:R.103 Water bridges: B:K.81 CM5.15: 14 residues within 4Å: Chain A: V.20, L.21 Chain B: V.164, I.226, V.230, E.231, R.234, F.245, I.246, Y.249, E.263, Q.267, L.271, L.274 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.164, B:I.226, B:F.245, B:I.246, B:Y.249, B:Y.249, B:Q.267, B:L.271, B:L.274, A:V.20, A:L.21 Hydrogen bonds: B:E.231, B:R.234, B:R.234 Salt bridges: B:R.234 CM5.16: 9 residues within 4Å: Chain B: P.15, S.16, L.18, L.32, S.35, R.38, L.39, F.346 Ligands: TMI.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.32, B:F.346 Hydrogen bonds: B:S.16, B:L.18, B:S.35 Salt bridges: B:R.38

Links

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Citation

Zhao, Y. et al., Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction. J.Biol.Chem. (2006)

Release Date

2005-12-27

Peptides

Cytochrome P450 2B4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome P450 2B4

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