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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "vdh"

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Search Summary

This query matches 8 Structures.

Refinements

Structure Determination Methodology

experimental (8)

Scientific Name of Source Organism

Pseudonocardia autotrophica (8)

Taxonomy

Bacteria (8)

Experimental Method

X-RAY DIFFRACTION (8)

Polymer Entity Type

Protein (8)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	2.0 - 2.5 (3)
	2.5 - 3.0 (2)
	3.0 - 3.5 (1)

Release Date

	2010 - 2014 (6)
	2015 - 2019 (2)

Enzyme Classification Name

Oxidoreductases (8)

Symmetry Type

Asymmetric (8)

SCOP Classification

All alpha proteins (8)

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1 to 8 of 8 Structures

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Explore in 3D

3A4G \| pdb_00003a4g	Download File View File

Structure of cytochrome P450 vdh from Pseudonocardia autotrophica (trigonal crystal form)

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-14
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	HEM, PG0

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3A4H \| pdb_00003a4h	Download File View File

Structure of cytochrome P450 vdh from Pseudonocardia autotrophica (orthorhombic crystal form)

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-14
Method	X-RAY DIFFRACTION 3.06 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	CA, HEM

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3A4Z \| pdb_00003a4z	Download File View File

Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-28
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	ACT, CA, GOL, HEM

Explore in 3D

3A50 \| pdb_00003a50	Download File View File

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

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-28
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	ACT, CA, GOL, HEM, VD3

Explore in 3D

3A51 \| pdb_00003a51	Download File View File

Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution with bound 25-hydroxyvitamin D3

Yasutake, Y., Fujii, Y., Cheon, W.K., Arisawa, A., Tamura, T.

(2010) J Biological Chem 285: 31193-31201

Released	2010-07-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D hydroxylase (protein)
Unique Ligands	ACT, CA, GOL, HEM, VDY

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3VRM \| pdb_00003vrm	Download File View File

Structure of cytochrome P450 Vdh mutant T107A with bound vitamin D3

Nishioka, T., Yasutake, Y., Tamura, T.

(2013) Chembiochem 14: 2284-2291

Released	2013-04-17
Method	X-RAY DIFFRACTION 2.57 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D(3) 25-hydroxylase (protein)
Unique Ligands	HEM, VD3

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5GNL \| pdb_00005gnl	Download File View File

Cytochrome P450 Vdh (CYP107BR1) F106V mutant

Yasutake, Y., Tamura, T.

(2017) Acta Crystallogr F Struct Biol Commun 73: 266-275

Released	2017-05-17
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D(3) 25-hydroxylase (protein)
Unique Ligands	HEM, PG0

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5GNM \| pdb_00005gnm	Download File View File

Cytochrome P450 Vdh (CYP107BR1) L348M mutant

Yasutake, Y., Tamura, T.

(2017) Acta Crystallogr F Struct Biol Commun 73: 266-275

Released	2017-05-17
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Pseudonocardia autotrophica
Macromolecule	Vitamin D(3) 25-hydroxylase (protein)
Unique Ligands	HEM

1 to 8 of 8 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

3A4G | pdb_00003a4g

Structure of cytochrome P450 vdh from Pseudonocardia autotrophica (trigonal crystal form)

3A4H | pdb_00003a4h

Structure of cytochrome P450 vdh from Pseudonocardia autotrophica (orthorhombic crystal form)

3A4Z | pdb_00003a4z

Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution

3A50 | pdb_00003a50

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

3A51 | pdb_00003a51

Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution with bound 25-hydroxyvitamin D3

3VRM | pdb_00003vrm

Structure of cytochrome P450 Vdh mutant T107A with bound vitamin D3

5GNL | pdb_00005gnl

Cytochrome P450 Vdh (CYP107BR1) F106V mutant

5GNM | pdb_00005gnm

Cytochrome P450 Vdh (CYP107BR1) L348M mutant

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

3A4G | pdb_00003a4g

3A4H | pdb_00003a4h

3A4Z | pdb_00003a4z

3A50 | pdb_00003a50

3A51 | pdb_00003a51

3VRM | pdb_00003vrm

5GNL | pdb_00005gnl

5GNM | pdb_00005gnm