SMTL ID : 3a50.2 (4 other biounits)

Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution with bound vitamin D3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

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

HEM.1: 29 residues within 4Å: Chain A: F.58, K.65, M.87, I.88, H.95, R.99, F.106, L.232, L.233, A.236, T.240, T.241, L.244, L.277, V.283, A.286, P.287, R.289, L.312, F.339, F.340, G.341, I.344, H.345, C.347, L.348, G.349, A.353 Ligands: VD3.2 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:I.88, A:F.106, A:L.232, A:A.236, A:L.244, A:L.277, A:V.283, A:L.312, A:F.340, A:L.348, A:L.348, A:A.353 Hydrogen bonds: A:P.287 Water bridges: A:H.345 Salt bridges: A:K.65, A:H.95, A:R.99, A:R.289, A:H.345 pi-Stacking: A:F.340 Metal complexes: A:C.347

1 x VD3: (1S,3Z)-3-[(2E)-2-[(1R,3AR,7AS)-7A-METHYL-1-[(2R)-6-METHYLHEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL(Non-covalent)

VD3.2: 12 residues within 4Å: Chain A: T.84, M.86, I.88, L.171, K.180, N.181, M.184, L.232, I.235, T.240, P.287 Ligands: HEM.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.84, A:I.88, A:L.171, A:K.180, A:L.232, A:I.235, A:I.235, A:T.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yasutake, Y. et al., Structural evidence for enhancement of sequential vitamin D3 hydroxylation activities by directed evolution of cytochrome P450 vitamin D3 hydroxylase. J.Biol.Chem. (2010)

Release Date

2010-07-28

Peptides

Vitamin D hydroxylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Vitamin D hydroxylase

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