Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3A50

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

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004497	molecular_function	monooxygenase activity
A	0005506	molecular_function	iron ion binding
A	0005737	cellular_component	cytoplasm
A	0016705	molecular_function	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
A	0020037	molecular_function	heme binding
A	0046872	molecular_function	metal ion binding
A	0047103	molecular_function	obsolete 3-alpha,7-alpha,12-alpha-trihydroxycholestan-26-al 26-oxidoreductase activity
A	0047748	molecular_function	cholestanetetraol 26-dehydrogenase activity
A	0047749	molecular_function	obsolete cholestanetriol 26-monooxygenase activity
B	0004497	molecular_function	monooxygenase activity
B	0005506	molecular_function	iron ion binding
B	0005737	cellular_component	cytoplasm
B	0016705	molecular_function	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
B	0020037	molecular_function	heme binding
B	0046872	molecular_function	metal ion binding
B	0047103	molecular_function	obsolete 3-alpha,7-alpha,12-alpha-trihydroxycholestan-26-al 26-oxidoreductase activity
B	0047748	molecular_function	cholestanetetraol 26-dehydrogenase activity
B	0047749	molecular_function	obsolete cholestanetriol 26-monooxygenase activity
C	0004497	molecular_function	monooxygenase activity
C	0005506	molecular_function	iron ion binding
C	0005737	cellular_component	cytoplasm
C	0016705	molecular_function	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
C	0020037	molecular_function	heme binding
C	0046872	molecular_function	metal ion binding
C	0047103	molecular_function	obsolete 3-alpha,7-alpha,12-alpha-trihydroxycholestan-26-al 26-oxidoreductase activity
C	0047748	molecular_function	cholestanetetraol 26-dehydrogenase activity
C	0047749	molecular_function	obsolete cholestanetriol 26-monooxygenase activity
D	0004497	molecular_function	monooxygenase activity
D	0005506	molecular_function	iron ion binding
D	0005737	cellular_component	cytoplasm
D	0016705	molecular_function	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
D	0020037	molecular_function	heme binding
D	0046872	molecular_function	metal ion binding
D	0047103	molecular_function	obsolete 3-alpha,7-alpha,12-alpha-trihydroxycholestan-26-al 26-oxidoreductase activity
D	0047748	molecular_function	cholestanetetraol 26-dehydrogenase activity
D	0047749	molecular_function	obsolete cholestanetriol 26-monooxygenase activity
E	0004497	molecular_function	monooxygenase activity
E	0005506	molecular_function	iron ion binding
E	0005737	cellular_component	cytoplasm
E	0016705	molecular_function	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
E	0020037	molecular_function	heme binding
E	0046872	molecular_function	metal ion binding
E	0047103	molecular_function	obsolete 3-alpha,7-alpha,12-alpha-trihydroxycholestan-26-al 26-oxidoreductase activity
E	0047748	molecular_function	cholestanetetraol 26-dehydrogenase activity
E	0047749	molecular_function	obsolete cholestanetriol 26-monooxygenase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	25
Details	BINDING SITE FOR RESIDUE HEM A 412

Chain	Residue
A	PHE58
A	THR240
A	THR241
A	ALA286
A	PRO287
A	ARG289
A	LEU312
A	PHE339
A	PHE340
A	GLY341
A	ILE344
A	LYS65
A	HIS345
A	CYS347
A	GLY349
A	ALA353
A	HOH428
A	VD32001
A	ILE88
A	HIS95
A	ARG99
A	PHE106
A	LEU232
A	LEU233
A	ALA236

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE VD3 A 2001

Chain	Residue
A	MET86
A	ILE88
A	LYS180
A	ASN181
A	LEU232
A	HEM412
A	HOH549

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACT A 4006

Chain	Residue
A	HIS342
A	GLY343
A	PHE346
D	HOH522
D	HOH693

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA A 2501

Chain	Residue
A	ASP204
A	HOH572
A	HOH596
A	HOH601
A	GOL3002
E	HOH695

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA A 2505

Chain	Residue
A	GLY128
A	HOH818
A	HOH993
A	HOH1027
B	HOH650

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CA A 2506

Chain	Residue
A	ASP320
D	ASP320
D	HOH892

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 3001

Chain	Residue
A	ASP53
A	GLU56
A	HOH452
A	HOH537
A	HOH575
D	ARG55
D	HOH425

site_id	AC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL A 3002

Chain	Residue
A	ASP204
A	SER209
A	HOH662
A	HOH989
A	CA2501
E	ARG70
E	PRO72
E	ALA304
E	HOH695
E	HOH1013

site_id	AC9
Number of Residues	25
Details	BINDING SITE FOR RESIDUE HEM B 412

Chain	Residue
B	PHE58
B	LYS65
B	ILE88
B	HIS95
B	ARG99
B	PHE106
B	LEU233
B	ALA236
B	THR240
B	THR241
B	VAL283
B	ALA286
B	PRO287
B	ARG289
B	LEU312
B	PHE339
B	PHE340
B	GLY341
B	ILE344
B	HIS345
B	CYS347
B	GLY349
B	ALA353
B	HOH425
B	VD32001

site_id	BC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE VD3 B 2001

Chain	Residue
B	ILE235
B	THR240
B	HEM412
B	THR84
B	MET86
B	LEU171
B	LYS180
B	ASN181
B	MET184

site_id	BC2
Number of Residues	26
Details	BINDING SITE FOR RESIDUE HEM C 412

Chain	Residue
C	PHE58
C	LYS65
C	MET87
C	ILE88
C	HIS95
C	ARG99
C	PHE106
C	LEU232
C	ALA236
C	THR240
C	THR241
C	ALA286
C	PRO287
C	ARG289
C	LEU312
C	PHE339
C	PHE340
C	GLY341
C	ILE344
C	HIS345
C	CYS347
C	LEU348
C	GLY349
C	ALA353
C	HOH427
C	VD32001

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE VD3 C 2001

Chain	Residue
C	THR84
C	MET86
C	LYS180
C	ASN181
C	ILE235
C	THR240
C	HEM412

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACT C 4004

Chain	Residue
A	ARG70
A	PRO72
A	HOH532
C	ASP204
C	HOH648
C	CA2503

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT C 4007

Chain	Residue
C	HIS342
C	GLY343
C	PHE346
C	HOH445

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA C 2503

Chain	Residue
A	HOH451
A	HOH532
C	ASP204
C	HOH437
C	HOH470
C	ACT4004

site_id	BC7
Number of Residues	25
Details	BINDING SITE FOR RESIDUE HEM D 412

Chain	Residue
D	PHE58
D	LYS65
D	MET87
D	ILE88
D	HIS95
D	ARG99
D	PHE106
D	ALA236
D	THR240
D	THR241
D	VAL283
D	ALA286
D	PRO287
D	ARG289
D	LEU312
D	PHE339
D	PHE340
D	GLY341
D	ILE344
D	HIS345
D	CYS347
D	GLY349
D	ALA353
D	HOH422
D	VD32001

site_id	BC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE VD3 D 2001

Chain	Residue
D	MET86
D	LYS180
D	ASN181
D	MET184
D	LEU232
D	ILE235
D	THR240
D	HEM412

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACT D 4001

Chain	Residue
D	HIS342
D	GLY343
D	PHE346
D	HOH457
D	HOH502

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CA D 2502

Chain	Residue
D	ASP204
D	HOH883
D	HOH884

site_id	CC2
Number of Residues	25
Details	BINDING SITE FOR RESIDUE HEM E 412

Chain	Residue
E	PHE58
E	LYS65
E	MET87
E	ILE88
E	HIS95
E	ARG99
E	PHE106
E	ALA236
E	THR240
E	THR241
E	VAL283
E	ALA286
E	PRO287
E	ARG289
E	LEU312
E	PHE339
E	PHE340
E	GLY341
E	ILE344
E	HIS345
E	CYS347
E	GLY349
E	ALA353
E	HOH422
E	VD32001

site_id	CC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE VD3 E 2001

Chain	Residue
E	ILE88
E	LYS180
E	ASN181
E	LEU232
E	LEU387
E	HEM412

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT E 4005

Chain	Residue
C	ARG70
E	ASP204
E	HOH888
E	CA2504

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT E 4008

Chain	Residue
E	HIS342
E	GLY343
E	PHE346

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA E 2504

Chain	Residue
C	HOH659
E	ASP204
E	HOH886
E	HOH887
E	ACT4005

Functional Information from PROSITE/UniProt

site_id	PS00086
Number of Residues	10
Details	CYTOCHROME_P450 Cytochrome P450 cysteine heme-iron ligand signature. FGhGIHFCLG

Chain	Residue	Details
A	PHE340-GLY349

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	5
Details	BINDING: axial binding residue => ECO:0000250\|UniProtKB:P0A512

Chain	Residue	Details
A	CYS347
B	CYS347
C	CYS347
D	CYS347
E	CYS347

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)