Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5K78

Dbr1 in complex with 16-mer branched RNA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000375	biological_process	RNA splicing, via transesterification reactions
A	0000398	biological_process	mRNA splicing, via spliceosome
A	0003723	molecular_function	RNA binding
A	0005506	molecular_function	iron ion binding
A	0005634	cellular_component	nucleus
A	0006397	biological_process	mRNA processing
A	0008270	molecular_function	zinc ion binding
A	0008419	molecular_function	RNA lariat debranching enzyme activity
A	0016787	molecular_function	hydrolase activity
A	0030145	molecular_function	manganese ion binding
A	0046872	molecular_function	metal ion binding
A	0048471	cellular_component	perinuclear region of cytoplasm
B	0000375	biological_process	RNA splicing, via transesterification reactions
B	0000398	biological_process	mRNA splicing, via spliceosome
B	0003723	molecular_function	RNA binding
B	0005506	molecular_function	iron ion binding
B	0005634	cellular_component	nucleus
B	0006397	biological_process	mRNA processing
B	0008270	molecular_function	zinc ion binding
B	0008419	molecular_function	RNA lariat debranching enzyme activity
B	0016787	molecular_function	hydrolase activity
B	0030145	molecular_function	manganese ion binding
B	0046872	molecular_function	metal ion binding
B	0048471	cellular_component	perinuclear region of cytoplasm
C	0000375	biological_process	RNA splicing, via transesterification reactions
C	0000398	biological_process	mRNA splicing, via spliceosome
C	0003723	molecular_function	RNA binding
C	0005506	molecular_function	iron ion binding
C	0005634	cellular_component	nucleus
C	0006397	biological_process	mRNA processing
C	0008270	molecular_function	zinc ion binding
C	0008419	molecular_function	RNA lariat debranching enzyme activity
C	0016787	molecular_function	hydrolase activity
C	0030145	molecular_function	manganese ion binding
C	0046872	molecular_function	metal ion binding
C	0048471	cellular_component	perinuclear region of cytoplasm
D	0000375	biological_process	RNA splicing, via transesterification reactions
D	0000398	biological_process	mRNA splicing, via spliceosome
D	0003723	molecular_function	RNA binding
D	0005506	molecular_function	iron ion binding
D	0005634	cellular_component	nucleus
D	0006397	biological_process	mRNA processing
D	0008270	molecular_function	zinc ion binding
D	0008419	molecular_function	RNA lariat debranching enzyme activity
D	0016787	molecular_function	hydrolase activity
D	0030145	molecular_function	manganese ion binding
D	0046872	molecular_function	metal ion binding
D	0048471	cellular_component	perinuclear region of cytoplasm
E	0000375	biological_process	RNA splicing, via transesterification reactions
E	0000398	biological_process	mRNA splicing, via spliceosome
E	0003723	molecular_function	RNA binding
E	0005506	molecular_function	iron ion binding
E	0005634	cellular_component	nucleus
E	0006397	biological_process	mRNA processing
E	0008270	molecular_function	zinc ion binding
E	0008419	molecular_function	RNA lariat debranching enzyme activity
E	0016787	molecular_function	hydrolase activity
E	0030145	molecular_function	manganese ion binding
E	0046872	molecular_function	metal ion binding
E	0048471	cellular_component	perinuclear region of cytoplasm

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue FE2 A 401

Chain	Residue
A	ASP45
A	ASN90
A	HIS180
A	HIS230
A	ZN402

site_id	AC2
Number of Residues	5
Details	binding site for residue ZN A 402

Chain	Residue
A	FE2401
A	CYS14
A	HIS16
A	ASP45
A	HIS232

site_id	AC3
Number of Residues	4
Details	binding site for residue SO4 A 403

Chain	Residue
A	ARG50
A	ASN95
A	HIS99
A	PRO146

site_id	AC4
Number of Residues	4
Details	binding site for residue SO4 A 404

Chain	Residue
A	LYS59
A	ILE132
A	LYS134
A	PHE155

site_id	AC5
Number of Residues	5
Details	binding site for residue FE2 B 401

Chain	Residue
B	ASP45
B	ASN90
B	HIS180
B	HIS230
B	ZN402

site_id	AC6
Number of Residues	5
Details	binding site for residue ZN B 402

Chain	Residue
B	CYS14
B	HIS16
B	ASP45
B	HIS232
B	FE2401

site_id	AC7
Number of Residues	3
Details	binding site for residue SO4 B 403

Chain	Residue
B	ARG50
B	ASN95
B	HIS99

site_id	AC8
Number of Residues	3
Details	binding site for residue SO4 B 404

Chain	Residue
B	THR307
B	LYS308
C	LYS215

site_id	AC9
Number of Residues	2
Details	binding site for residue SO4 B 405

Chain	Residue
B	LYS305
B	HIS355

site_id	AD1
Number of Residues	6
Details	binding site for residue FE2 C 401

Chain	Residue
C	ASP45
C	ASN90
C	HIS180
C	HIS230
C	ZN402
x	G510

site_id	AD2
Number of Residues	6
Details	binding site for residue ZN C 402

Chain	Residue
C	CYS14
C	HIS16
C	ASP45
C	HIS232
C	FE2401
x	G510

site_id	AD3
Number of Residues	3
Details	binding site for residue SO4 C 403

Chain	Residue
C	ARG50
C	ASN95
C	HIS99

site_id	AD4
Number of Residues	2
Details	binding site for residue SO4 C 404

Chain	Residue
C	SER172
C	GLN173

site_id	AD5
Number of Residues	4
Details	binding site for residue SO4 C 405

Chain	Residue
C	LYS18
C	TYR64
C	LYS249
X	A501

site_id	AD6
Number of Residues	5
Details	binding site for residue SO4 C 406

Chain	Residue
C	LYS320
C	TYR321
D	TYR51
D	TYR74
D	THR332

site_id	AD7
Number of Residues	6
Details	binding site for residue FE2 D 401

Chain	Residue
D	ASP45
D	ASN90
D	HIS180
D	HIS230
D	ZN402
y	G510

site_id	AD8
Number of Residues	6
Details	binding site for residue ZN D 402

Chain	Residue
D	CYS14
D	HIS16
D	ASP45
D	HIS232
D	FE2401
y	G510

site_id	AD9
Number of Residues	5
Details	binding site for residue SO4 D 403

Chain	Residue
D	ARG50
D	TYR57
D	ASN95
D	HIS99
D	PRO146

site_id	AE1
Number of Residues	2
Details	binding site for residue SO4 D 404

Chain	Residue
D	SER172
D	GLN173

site_id	AE2
Number of Residues	3
Details	binding site for residue SO4 D 405

Chain	Residue
D	ARG20
D	GLU21
D	ARG24

site_id	AE3
Number of Residues	5
Details	binding site for residue FE2 E 401

Chain	Residue
E	ASP45
E	ASN90
E	HIS180
E	HIS230
E	ZN402

site_id	AE4
Number of Residues	5
Details	binding site for residue ZN E 402

Chain	Residue
E	CYS14
E	HIS16
E	ASP45
E	HIS232
E	FE2401

site_id	AE5
Number of Residues	4
Details	binding site for residue SO4 E 403

Chain	Residue
E	ARG50
E	ASN95
E	HIS99
E	PRO146

site_id	AE6
Number of Residues	20
Details	binding site for Di-nucleotide G x 510 and A X 501

Chain	Residue
C	LYS18
C	ASP45
C	GLN47
C	TYR64
C	ASN90
C	GLY201
C	PHE202
C	ASP205
C	LEU209
C	HIS230
C	MET231
C	HIS232
C	LYS249
C	FE2401
C	ZN402
C	SO4405
X	A500
X	C502
x	U511
C	HIS16

site_id	AE7
Number of Residues	21
Details	binding site for Di-nucleotide G y 510 and A Y 501

Chain	Residue
D	HIS16
D	ASP45
D	GLN47
D	VAL60
D	PRO61
D	LYS63
D	TYR64
D	ASN90
D	GLY201
D	PHE202
D	ASP205
D	LEU209
D	HIS230
D	MET231
D	HIS232
D	LYS249
D	FE2401
D	ZN402
Y	A500
Y	C502
y	U511

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	140
Details	Region: {"description":"Lariat recognition loop","evidences":[{"source":"PubMed","id":"27930312","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	10
Details	Binding site: {"evidences":[{"source":"PubMed","id":"27930312","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28504306","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5K73","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5K77","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5K78","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5UKI","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	10
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25123664","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27930312","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28504306","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4PEF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4PEG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4PEH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4PEI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5K73","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5K77","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5K78","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5UKI","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	15
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25123664","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"AUG-2022","submissionDatabase":"PDB data bank","title":"Dbr1 in complex with 5-mer cleavage product.","authors":["Clark N.E.","Taylor A.B."]}},{"source":"PDB","id":"4PEH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8DZK","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	5
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25123664","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"AUG-2022","submissionDatabase":"PDB data bank","title":"Dbr1 in complex with 5-mer cleavage product.","authors":["Clark N.E.","Taylor A.B."]}},{"source":"PDB","id":"4PEG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4PEI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8DZK","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	5
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25123664","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4PEG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4PEI","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	10
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25123664","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27930312","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4PEG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4PEI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5K77","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5K78","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	5
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25123664","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27930312","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4PEG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4PEH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4PEI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5K77","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5K78","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	10
Details	Binding site: {"evidences":[{"source":"PubMed","id":"27930312","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4PEG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4PEI","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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