SMTL ID : 2nnh.3 (2 other biounits)

CYP2C8dH complexed with 2 molecules of 9-cis retinoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: R.114, N.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.115 Salt bridges: A:R.114 SO4.6: 2 residues within 4Å: Chain B: R.114, N.115 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.115 Salt bridges: B:R.114

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

HEM.2: 25 residues within 4Å: Chain A: R.79, I.94, I.95, W.102, R.106, I.160, A.279, G.280, T.283, T.284, T.287, Q.338, L.343, V.348, H.350, P.409, F.410, S.411, R.415, C.417, A.418, G.419, L.422, A.423 Ligands: 9CR.3 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:I.94, A:I.160, A:L.343, A:V.348, A:F.410, A:F.410, A:A.418, A:L.422, A:A.423 Hydrogen bonds: A:S.411 Water bridges: A:V.348 Salt bridges: A:R.79, A:R.79, A:R.106, A:H.350, A:R.415 Metal complexes: A:C.417 HEM.7: 26 residues within 4Å: Chain B: R.79, I.94, I.95, W.102, R.106, L.113, L.276, A.279, G.280, T.283, T.284, T.287, Q.338, L.343, V.348, H.350, P.409, F.410, S.411, R.415, C.417, A.418, G.419, A.423, E.426 Ligands: 9CR.8 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:I.94, B:L.113, B:L.276, B:L.343, B:V.348, B:F.410, B:F.410, B:A.418 Hydrogen bonds: B:S.411 Water bridges: B:V.348 Salt bridges: B:R.79, B:R.79, B:R.106, B:H.350, B:R.415 Metal complexes: B:C.417

4 x 9CR: (9cis)-retinoic acid(Non-covalent)

9CR.3: 15 residues within 4Å: Chain A: R.79, G.80, N.81, S.82, S.85, I.95, S.96, V.278, A.279, T.283, V.348, P.349, I.458 Ligands: HEM.2, 9CR.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.95, A:I.95, A:A.279, A:T.283, A:V.348, A:V.348, A:P.349, A:I.458 Hydrogen bonds: A:G.80, A:N.81, A:S.82, A:P.349 9CR.4: 14 residues within 4Å: Chain A: S.82, I.84, S.85, I.88, N.186, F.187, L.190, N.191, N.199, V.219, R.223, V.278, I.458 Ligands: 9CR.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.84, A:I.84, A:F.187, A:L.190, A:L.190, A:N.191, A:V.278, A:V.278, A:I.458 Hydrogen bonds: A:N.186 Salt bridges: A:R.223 9CR.8: 13 residues within 4Å: Chain B: R.79, G.80, N.81, S.82, I.95, V.278, T.283, V.348, P.349, I.458, V.459 Ligands: HEM.7, 9CR.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.79, B:I.95, B:T.283, B:V.348, B:V.348, B:P.349, B:I.458 Hydrogen bonds: B:G.80, B:N.81, B:S.82, B:P.349 9CR.9: 13 residues within 4Å: Chain B: S.82, I.84, I.88, F.183, N.186, F.187, L.190, N.191, N.199, R.223, V.278, I.458 Ligands: 9CR.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.84, B:I.88, B:N.186, B:F.187, B:L.190, B:L.190, B:N.191, B:V.278, B:V.278, B:I.458 Hydrogen bonds: B:N.186 Salt bridges: B:R.223

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 13 residues within 4Å: Chain A: F.208, P.209, G.210, T.211 Chain B: I.84, R.87, I.88, W.194, F.208, T.211, H.212, V.215, L.216 14 PLIP interactions: 3 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:F.208, B:I.84, B:I.84, B:R.87, B:I.88, B:W.194, B:W.194, B:F.208, B:F.208, B:F.208, B:V.215, B:L.216 Hydrogen bonds: A:G.210, A:T.211 PLM.10: 13 residues within 4Å: Chain A: I.84, R.87, I.88, W.194, C.198, F.208, T.211, H.212, L.216 Chain B: F.208, P.209, G.210, T.211 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.84, A:I.84, A:R.87, A:I.88, A:F.208, A:F.208, A:L.216 Water bridges: A:S.192 Hydrogen bonds: B:G.210, B:T.211, B:T.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schoch, G.A. et al., Determinants of cytochrome P450 2C8 substrate binding: structures of complexes with montelukast, troglitazone, felodipine, and 9-cis-retinoic acid. J.Biol.Chem. (2008)

Release Date

2007-10-23

Peptides

Cytochrome P450 2C8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytochrome P450 2C8

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