SMTL ID : 3vrm.1

Structure of cytochrome P450 Vdh mutant T107A with bound vitamin D3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.57 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, P.282, V.283, A.286, P.287, R.289, L.312, F.339, F.340, G.341, H.345, C.347, L.348, G.349, A.353 Ligands: VD3.2 20 PLIP interactions: 20 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 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]ETHYLI DENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL(Non-covalent)

VD3.2: 7 residues within 4Å: Chain A: L.171, I.235, A.236, P.287, I.288, L.387 Ligands: HEM.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.235, A:A.236, A:P.287, A:I.288, A:L.387

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yasutake, Y. et al., A single mutation at the ferredoxin binding site of p450 vdh enables efficient biocatalytic production of 25-hydroxyvitamin d3. Chembiochem (2013)

Release Date

2013-04-17

Peptides

Vitamin D(3) 25-hydroxylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Vitamin D(3) 25-hydroxylase