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

Crystal structure of the cysteine depleted CYP3A4 bound to glycerol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 28 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 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:I.98, A:F.117, A:F.282, A:A.285, 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:E.354 Salt bridges: A:R.85, A:R.85, A:R.110, A:R.355, A:R.420 Metal complexes: A:C.422, H2O.1 HEM.14: 28 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.15 22 PLIP interactions: 21 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:I.98, B:F.117, B:F.282, B:A.285, 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:E.354 Salt bridges: B:R.85, B:R.85, B:R.110, B:R.355, B:R.420 Metal complexes: B:C.422, H2O.5 HEM.27: 28 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, F.427, A.428, M.432 Ligands: GOL.28 22 PLIP interactions: 21 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:I.98, C:F.117, C:F.282, C:A.285, C:V.293, C:I.349, C:A.350, C:L.353, C:F.415, C:F.415, C:I.423, C:F.427 Hydrogen bonds: C:S.417 Water bridges: C:R.85, C:E.354 Salt bridges: C:R.85, C:R.85, C:R.110, C:R.355, C:R.420 Metal complexes: C:C.422, H2O.9 HEM.40: 28 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, F.427, A.428, M.432 Ligands: GOL.41 22 PLIP interactions: 21 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: D:I.98, D:F.117, D:F.282, D:A.285, D:V.293, D:I.349, D:A.350, D:L.353, D:F.415, D:F.415, D:I.423, D:F.427 Hydrogen bonds: D:S.417 Water bridges: D:R.85, D:E.354 Salt bridges: D:R.85, D:R.85, D:R.110, D:R.355, D:R.420 Metal complexes: D:C.422, H2O.14

48 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: S.99, R.192, F.284, A.285 Ligands: HEM.1 Ligand excluded by PLIP GOL.3: 6 residues within 4Å: Chain A: F.13, K.14, I.18, G.20, T.22, Y.55 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: P.21, T.22, L.24, N.29, L.31, S.32 Ligand excluded by PLIP GOL.5: 11 residues within 4Å: Chain A: K.35, G.36, F.37, A.38, M.39, M.351, S.458, G.460, G.461, L.462, L.463 Ligand excluded by PLIP GOL.6: 9 residues within 4Å: Chain A: Y.33, F.37, D.56, R.86, F.195, F.200, L.201, T.204, R.352 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: Y.387, W.388, T.389, R.398 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: T.303, H.304, P.305, D.306 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: K.310, E.314, E.334, Y.335, M.338, E.397 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: K.189, L.190, L.191, F.193, V.220, P.222, F.284 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: Q.309, Q.312, E.313, D.316, S.444, R.476 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: P.385, K.386, Y.387, W.388, T.389 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain A: K.153, E.288, S.291, S.292, Q.464, P.465 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain B: S.99, R.192, F.284, A.285 Ligands: HEM.14 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain B: F.13, K.14, I.18, G.20, T.22, Y.55 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: P.21, T.22, L.24, N.29, L.31, S.32 Ligand excluded by PLIP GOL.18: 11 residues within 4Å: Chain B: K.35, G.36, F.37, A.38, M.39, M.351, S.458, G.460, G.461, L.462, L.463 Ligand excluded by PLIP GOL.19: 9 residues within 4Å: Chain B: Y.33, F.37, D.56, R.86, F.195, F.200, L.201, T.204, R.352 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: Y.387, W.388, T.389, R.398 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain B: T.303, H.304, P.305, D.306 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: K.310, E.314, E.334, Y.335, M.338, E.397 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain B: K.189, L.190, L.191, F.193, V.220, P.222, F.284 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain B: Q.309, Q.312, E.313, D.316, S.444, R.476 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain B: P.385, K.386, Y.387, W.388, T.389 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain B: K.153, E.288, S.291, S.292, Q.464, P.465 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain C: S.99, R.192, F.284, A.285 Ligands: HEM.27 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain C: F.13, K.14, I.18, G.20, T.22, Y.55 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain C: P.21, T.22, L.24, N.29, L.31, S.32 Ligand excluded by PLIP GOL.31: 11 residues within 4Å: Chain C: K.35, G.36, F.37, A.38, M.39, M.351, S.458, G.460, G.461, L.462, L.463 Ligand excluded by PLIP GOL.32: 9 residues within 4Å: Chain C: Y.33, F.37, D.56, R.86, F.195, F.200, L.201, T.204, R.352 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain C: Y.387, W.388, T.389, R.398 Ligand excluded by PLIP GOL.34: 4 residues within 4Å: Chain C: T.303, H.304, P.305, D.306 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain C: K.310, E.314, E.334, Y.335, M.338, E.397 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain C: K.189, L.190, L.191, F.193, V.220, P.222, F.284 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain C: Q.309, Q.312, E.313, D.316, S.444, R.476 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain C: P.385, K.386, Y.387, W.388, T.389 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain C: K.153, E.288, S.291, S.292, Q.464, P.465 Ligand excluded by PLIP GOL.41: 5 residues within 4Å: Chain D: S.99, R.192, F.284, A.285 Ligands: HEM.40 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain D: F.13, K.14, I.18, G.20, T.22, Y.55 Ligand excluded by PLIP GOL.43: 6 residues within 4Å: Chain D: P.21, T.22, L.24, N.29, L.31, S.32 Ligand excluded by PLIP GOL.44: 11 residues within 4Å: Chain D: K.35, G.36, F.37, A.38, M.39, M.351, S.458, G.460, G.461, L.462, L.463 Ligand excluded by PLIP GOL.45: 9 residues within 4Å: Chain D: Y.33, F.37, D.56, R.86, F.195, F.200, L.201, T.204, R.352 Ligand excluded by PLIP GOL.46: 4 residues within 4Å: Chain D: Y.387, W.388, T.389, R.398 Ligand excluded by PLIP GOL.47: 4 residues within 4Å: Chain D: T.303, H.304, P.305, D.306 Ligand excluded by PLIP GOL.48: 6 residues within 4Å: Chain D: K.310, E.314, E.334, Y.335, M.338, E.397 Ligand excluded by PLIP GOL.49: 7 residues within 4Å: Chain D: K.189, L.190, L.191, F.193, V.220, P.222, F.284 Ligand excluded by PLIP GOL.50: 6 residues within 4Å: Chain D: Q.309, Q.312, E.313, D.316, S.444, R.476 Ligand excluded by PLIP GOL.51: 5 residues within 4Å: Chain D: P.385, K.386, Y.387, W.388, T.389 Ligand excluded by PLIP GOL.52: 6 residues within 4Å: Chain D: K.153, E.288, S.291, S.292, Q.464, P.465 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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Cytochrome P450 3A4

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