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

Crystal structure of human CYP3A4 bound to glycerol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 29 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, F.427, A.428, M.432 Ligands: GOL.2, EDO.11 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:I.98, A:F.117, A:F.282, A:V.293, A:I.349, A:A.350, A:L.353, A:F.415, A:F.415, A:I.423, A:F.427 Hydrogen bonds: A:S.417 Water bridges: A:R.85, A:R.355 Salt bridges: A:R.85, A:R.85, A:R.110, A:R.355, A:R.420 Metal complexes: A:C.422, H2O.4 HEM.22: 29 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, F.427, A.428, M.432 Ligands: GOL.23, EDO.32 21 PLIP interactions: 20 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:I.98, B:F.117, B:F.282, B:V.293, B:I.349, B:A.350, B:L.353, B:F.415, B:F.415, B:I.423, B:F.427 Hydrogen bonds: B:S.417 Water bridges: B:R.85, B:R.355 Salt bridges: B:R.85, B:R.85, B:R.110, B:R.355, B:R.420 Metal complexes: B:C.422, H2O.16

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: R.85, S.99, R.192, F.284, A.285 Ligands: HEM.1, EDO.11, EDO.12 Ligand excluded by PLIP GOL.3: 6 residues within 4Å: Chain A: P.21, S.32, F.40, E.43, K.47, Y.48 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: P.21, T.22, L.24, N.29, L.31, S.32 Ligands: EDO.13 Ligand excluded by PLIP GOL.5: 11 residues within 4Å: Chain A: G.36, F.37, C.38, M.351, L.457, S.458, G.460, G.461, L.462, L.463, Q.464 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: I.30, L.31, Y.33, H.34, L.196, L.201 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: K.310, E.334, Y.335, M.338, E.397 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: D.360, V.361, E.362, F.367 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: P.305, Q.308, Q.309, Q.312, S.444 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain B: R.85, S.99, R.192, F.284, A.285 Ligands: HEM.22, EDO.32, EDO.33 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain B: P.21, S.32, F.40, E.43, K.47, Y.48 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain B: P.21, T.22, L.24, N.29, L.31, S.32 Ligands: EDO.34 Ligand excluded by PLIP GOL.26: 11 residues within 4Å: Chain B: G.36, F.37, C.38, M.351, L.457, S.458, G.460, G.461, L.462, L.463, Q.464 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain B: I.30, L.31, Y.33, H.34, L.196, L.201 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain B: K.310, E.334, Y.335, M.338, E.397 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain B: D.360, V.361, E.362, F.367 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain B: P.305, Q.308, Q.309, Q.312, S.444 Ligand excluded by PLIP

24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 5 residues within 4Å: Chain A: F.13, I.18, G.20, T.22, Y.55 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: R.192, T.289, A.350 Ligands: HEM.1, GOL.2 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: S.99, I.100, R.192, F.193, I.281, F.284 Ligands: GOL.2 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: L.31, S.32 Ligands: GOL.4 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: Y.387, W.388, T.389, R.398 Ligands: EDO.18 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: K.153, G.157, L.191, Y.287, S.291 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain A: Q.259, S.261 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: L.331, E.334, D.337, K.433 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: Y.387, W.388, N.406, I.407, D.408, I.411 Ligands: EDO.14 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: I.164, T.167, S.168, F.251, F.282, G.286 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: D.56, G.57, Q.58, Q.59, T.204, P.207 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: F.347, R.383, L.457 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: F.13, I.18, G.20, T.22, Y.55 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain B: R.192, T.289, A.350 Ligands: HEM.22, GOL.23 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain B: S.99, I.100, R.192, F.193, I.281, F.284 Ligands: GOL.23 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain B: L.31, S.32 Ligands: GOL.25 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain B: Y.387, W.388, T.389, R.398 Ligands: EDO.39 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain B: K.153, G.157, L.191, Y.287, S.291 Ligand excluded by PLIP EDO.37: 2 residues within 4Å: Chain B: Q.259, S.261 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain B: L.331, E.334, D.337, K.433 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain B: Y.387, W.388, N.406, I.407, D.408, I.411 Ligands: EDO.35 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain B: I.164, T.167, S.168, F.251, F.282, G.286 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain B: D.56, G.57, Q.58, Q.59, T.204, P.207 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain B: F.347, R.383, L.457 Ligand excluded by PLIP

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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