Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3FY4

(6-4) Photolyase Crystal Structure

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003677	molecular_function	DNA binding
A	0003904	molecular_function	deoxyribodipyrimidine photo-lyase activity
A	0003914	molecular_function	DNA (6-4) photolyase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0006139	biological_process	nucleobase-containing compound metabolic process
A	0006281	biological_process	DNA repair
A	0006290	biological_process	pyrimidine dimer repair
A	0006974	biological_process	DNA damage response
A	0009411	biological_process	response to UV
A	0009416	biological_process	response to light stimulus
A	0009507	cellular_component	chloroplast
A	0016829	molecular_function	lyase activity
A	0032922	biological_process	circadian regulation of gene expression
A	0042644	cellular_component	chloroplast nucleoid
A	0043153	biological_process	entrainment of circadian clock by photoperiod
A	0071949	molecular_function	FAD binding
B	0000166	molecular_function	nucleotide binding
B	0003677	molecular_function	DNA binding
B	0003904	molecular_function	deoxyribodipyrimidine photo-lyase activity
B	0003914	molecular_function	DNA (6-4) photolyase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0006139	biological_process	nucleobase-containing compound metabolic process
B	0006281	biological_process	DNA repair
B	0006290	biological_process	pyrimidine dimer repair
B	0006974	biological_process	DNA damage response
B	0009411	biological_process	response to UV
B	0009416	biological_process	response to light stimulus
B	0009507	cellular_component	chloroplast
B	0016829	molecular_function	lyase activity
B	0032922	biological_process	circadian regulation of gene expression
B	0042644	cellular_component	chloroplast nucleoid
B	0043153	biological_process	entrainment of circadian clock by photoperiod
B	0071949	molecular_function	FAD binding
C	0000166	molecular_function	nucleotide binding
C	0003677	molecular_function	DNA binding
C	0003904	molecular_function	deoxyribodipyrimidine photo-lyase activity
C	0003914	molecular_function	DNA (6-4) photolyase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0006139	biological_process	nucleobase-containing compound metabolic process
C	0006281	biological_process	DNA repair
C	0006290	biological_process	pyrimidine dimer repair
C	0006974	biological_process	DNA damage response
C	0009411	biological_process	response to UV
C	0009416	biological_process	response to light stimulus
C	0009507	cellular_component	chloroplast
C	0016829	molecular_function	lyase activity
C	0032922	biological_process	circadian regulation of gene expression
C	0042644	cellular_component	chloroplast nucleoid
C	0043153	biological_process	entrainment of circadian clock by photoperiod
C	0071949	molecular_function	FAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE IMD A 901

Chain	Residue
A	TRP408
A	PHE415
A	TYR422
B	LYS208

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE IMD A 902

Chain	Residue
A	ASN330
A	ASP378
A	LEU379
A	LYS492

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IMD A 905

Chain	Residue
A	PRO255
A	TRP359
A	PHE252

site_id	AC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE MES A 920

Chain	Residue
A	LYS244
A	PRO245
A	PRO292
A	VAL293
A	GLN298
A	TRP301
A	HIS364
A	HIS368
A	ASN405

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PO4 A 930

Chain	Residue
A	PHE242
A	GLU243

site_id	AC6
Number of Residues	27
Details	BINDING SITE FOR RESIDUE FAD A 900

Chain	Residue
A	LYS244
A	THR257
A	THR258
A	VAL259
A	MET260
A	SER261
A	LEU264
A	GLN298
A	TRP301
A	ARG302
A	PHE305
A	TRP361
A	HIS364
A	ARG367
A	HIS368
A	PHE390
A	LEU394
A	ASP396
A	SER397
A	ASP398
A	ILE401
A	ASN402
A	ASN405
A	TRP406
A	LEU409
A	HOH3199
A	HOH3354

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE IMD C 901

Chain	Residue
C	TRP408
C	PHE415
C	ARG420
C	TYR422
C	HOH3357

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE IMD C 902

Chain	Residue
C	ASN330
C	ASP378
C	ALA485
C	LYS492

site_id	AC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE MES C 920

Chain	Residue
C	LYS244
C	PRO245
C	PRO292
C	TRP301
C	HIS364
C	HIS368
C	ASN405
C	TRP408
C	FAD900
C	HOH3135

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 C 930

Chain	Residue
C	TRP238
C	PHE242
C	GLU243
C	LYS246
C	HOH3286

site_id	BC2
Number of Residues	29
Details	BINDING SITE FOR RESIDUE FAD C 900

Chain	Residue
C	HOH3013
C	HOH3047
C	HOH3136
C	LYS244
C	THR257
C	THR258
C	VAL259
C	MET260
C	SER261
C	LEU264
C	GLN298
C	TRP301
C	ARG302
C	PHE305
C	TRP361
C	HIS364
C	ARG367
C	HIS368
C	PHE390
C	LEU394
C	ASP396
C	SER397
C	ASP398
C	ILE401
C	ASN402
C	ASN405
C	TRP406
C	LEU409
C	MES920

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE IMD B 901

Chain	Residue
B	TRP408
B	PHE415
B	ARG420
B	TYR422
C	LYS208

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE IMD B 904

Chain	Residue
B	LYS325
B	TYR416

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IMD B 905

Chain	Residue
B	PHE252
B	PRO255
B	TRP359

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE IMD B 906

Chain	Residue
B	LEU229
B	THR230
B	ILE233
B	TYR273
B	CYS277

site_id	BC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE MES B 920

Chain	Residue
B	LYS244
B	PRO245
B	PRO292
B	GLN298
B	TRP301
B	HIS364
B	HIS368
B	ASN405

site_id	BC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PO4 B 930

Chain	Residue
B	TRP238
B	GLU243

site_id	BC9
Number of Residues	28
Details	BINDING SITE FOR RESIDUE FAD B 900

Chain	Residue
B	LYS244
B	THR257
B	THR258
B	VAL259
B	MET260
B	SER261
B	LEU264
B	GLN298
B	TRP301
B	ARG302
B	PHE305
B	TRP361
B	MET362
B	HIS364
B	ARG367
B	HIS368
B	PHE390
B	LEU394
B	ASP396
B	SER397
B	ASP398
B	ILE401
B	ASN402
B	ASN405
B	TRP406
B	LEU409
B	HOH3138
B	HOH3153

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	276
Details	Domain: {"description":"Photolyase/cryptochrome alpha/beta"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	15
Details	Region: {"description":"Interaction with DNA","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	3
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	48
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19359474","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	6
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	9
Details	Site: {"description":"Electron transfer via tryptophanyl radical","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	3
Details	Annotated By Reference To The Literature 1dnp

Chain	Residue	Details
A	TRP383
A	TRP406
A	TRP329

site_id	CSA2
Number of Residues	3
Details	Annotated By Reference To The Literature 1dnp

Chain	Residue	Details
B	TRP383
B	TRP406
B	TRP329

site_id	CSA3
Number of Residues	3
Details	Annotated By Reference To The Literature 1dnp

Chain	Residue	Details
C	TRP383
C	TRP406
C	TRP329

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