Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1ZBU

crystal structure of full-length 3'-exonuclease

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000175	molecular_function	3'-5'-RNA exonuclease activity
A	0000460	biological_process	maturation of 5.8S rRNA
A	0000467	biological_process	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
A	0003676	molecular_function	nucleic acid binding
A	0003723	molecular_function	RNA binding
A	0004527	molecular_function	exonuclease activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005730	cellular_component	nucleolus
A	0005737	cellular_component	cytoplasm
A	0006364	biological_process	rRNA processing
A	0008408	molecular_function	3'-5' exonuclease activity
A	0019843	molecular_function	rRNA binding
A	0031047	biological_process	regulatory ncRNA-mediated gene silencing
A	0031125	biological_process	rRNA 3'-end processing
A	0043022	molecular_function	ribosome binding
A	0046872	molecular_function	metal ion binding
A	0071044	biological_process	histone mRNA catabolic process
A	0071204	cellular_component	histone pre-mRNA 3'end processing complex
A	0071207	molecular_function	histone pre-mRNA stem-loop binding
B	0000175	molecular_function	3'-5'-RNA exonuclease activity
B	0000460	biological_process	maturation of 5.8S rRNA
B	0000467	biological_process	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
B	0003676	molecular_function	nucleic acid binding
B	0003723	molecular_function	RNA binding
B	0004527	molecular_function	exonuclease activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005730	cellular_component	nucleolus
B	0005737	cellular_component	cytoplasm
B	0006364	biological_process	rRNA processing
B	0008408	molecular_function	3'-5' exonuclease activity
B	0019843	molecular_function	rRNA binding
B	0031047	biological_process	regulatory ncRNA-mediated gene silencing
B	0031125	biological_process	rRNA 3'-end processing
B	0043022	molecular_function	ribosome binding
B	0046872	molecular_function	metal ion binding
B	0071044	biological_process	histone mRNA catabolic process
B	0071204	cellular_component	histone pre-mRNA 3'end processing complex
B	0071207	molecular_function	histone pre-mRNA stem-loop binding
C	0000175	molecular_function	3'-5'-RNA exonuclease activity
C	0000460	biological_process	maturation of 5.8S rRNA
C	0000467	biological_process	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
C	0003676	molecular_function	nucleic acid binding
C	0003723	molecular_function	RNA binding
C	0004527	molecular_function	exonuclease activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005730	cellular_component	nucleolus
C	0005737	cellular_component	cytoplasm
C	0006364	biological_process	rRNA processing
C	0008408	molecular_function	3'-5' exonuclease activity
C	0019843	molecular_function	rRNA binding
C	0031047	biological_process	regulatory ncRNA-mediated gene silencing
C	0031125	biological_process	rRNA 3'-end processing
C	0043022	molecular_function	ribosome binding
C	0046872	molecular_function	metal ion binding
C	0071044	biological_process	histone mRNA catabolic process
C	0071204	cellular_component	histone pre-mRNA 3'end processing complex
C	0071207	molecular_function	histone pre-mRNA stem-loop binding
D	0000175	molecular_function	3'-5'-RNA exonuclease activity
D	0000460	biological_process	maturation of 5.8S rRNA
D	0000467	biological_process	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
D	0003676	molecular_function	nucleic acid binding
D	0003723	molecular_function	RNA binding
D	0004527	molecular_function	exonuclease activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005730	cellular_component	nucleolus
D	0005737	cellular_component	cytoplasm
D	0006364	biological_process	rRNA processing
D	0008408	molecular_function	3'-5' exonuclease activity
D	0019843	molecular_function	rRNA binding
D	0031047	biological_process	regulatory ncRNA-mediated gene silencing
D	0031125	biological_process	rRNA 3'-end processing
D	0043022	molecular_function	ribosome binding
D	0046872	molecular_function	metal ion binding
D	0071044	biological_process	histone mRNA catabolic process
D	0071204	cellular_component	histone pre-mRNA 3'end processing complex
D	0071207	molecular_function	histone pre-mRNA stem-loop binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG A 1000

Chain	Residue
A	ASP134
A	ASP234
A	MG1001
A	AMP1002

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 1001

Chain	Residue
A	AMP1002
A	ASP134
A	PHE135
A	GLU136
A	ASP298
A	MG1000

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 2000

Chain	Residue
B	ASP134
B	PHE135
B	ASP234
B	MG2001
B	AMP2002

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 2001

Chain	Residue
B	ASP134
B	GLU136
B	ASP298
B	MG2000
B	AMP2002

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG C 3000

Chain	Residue
C	ASP134
C	PHE135
C	ASP234
C	AMP3002

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG C 3001

Chain	Residue
C	ASP134
C	GLU136
C	ASP298
C	AMP3002

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 4000

Chain	Residue
D	ASP134
D	ASP230
D	TRP233
D	ASP234
D	MG4001
D	AMP4002

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 4001

Chain	Residue
D	ASP134
D	PHE135
D	ASP234
D	MG4000
D	AMP4002

site_id	AC9
Number of Residues	12
Details	BINDING SITE FOR RESIDUE AMP A 1002

Chain	Residue
A	ASP134
A	PHE135
A	GLU136
A	ALA137
A	THR138
A	CYS139
A	ASN143
A	PHE185
A	PHE238
A	HIS293
A	MG1000
A	MG1001

site_id	BC1
Number of Residues	12
Details	BINDING SITE FOR RESIDUE AMP B 2002

Chain	Residue
B	ASP134
B	PHE135
B	GLU136
B	ALA137
B	THR138
B	CYS139
B	ASN143
B	PHE185
B	PHE238
B	HIS293
B	MG2000
B	MG2001

site_id	BC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE AMP C 3002

Chain	Residue
C	ASP134
C	PHE135
C	GLU136
C	ALA137
C	THR138
C	CYS139
C	ASN143
C	PHE185
C	PHE238
C	HIS293
C	MG3000
C	MG3001

site_id	BC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE AMP D 4002

Chain	Residue
D	PHE135
D	GLU136
D	ALA137
D	THR138
D	CYS139
D	ASN143
D	PHE185
D	THR190
D	TRP233
D	PHE238
D	HIS293
D	MG4000
D	MG4001

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	ACT_SITE: Proton acceptor => ECO:0000269\|PubMed:15451662, ECO:0007744\|PDB:1W0H

Chain	Residue	Details
A	ALA137
A	CYS294
B	ALA137
B	CYS294
C	ALA137
C	CYS294
D	ALA137
D	CYS294

site_id	SWS_FT_FI2
Number of Residues	24
Details	BINDING: BINDING => ECO:0000269\|PubMed:15451662, ECO:0007744\|PDB:1W0H

Chain	Residue	Details
A	PHE135
B	MSE235
B	CYS294
B	SER299
C	PHE135
C	ALA137
C	THR138
C	MSE235
C	CYS294
C	SER299
D	PHE135
A	ALA137
D	ALA137
D	THR138
D	MSE235
D	CYS294
D	SER299
A	THR138
A	MSE235
A	CYS294
A	SER299
B	PHE135
B	ALA137
B	THR138

site_id	SWS_FT_FI3
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	ASP60
B	ASP60
C	ASP60
D	ASP60

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:19690332, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	ASP63
B	ASP63
C	ASP63
D	ASP63

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	5
Details	M-CSA 784

Chain	Residue	Details
A	PHE135	metal ligand
A	ALA137	electrostatic stabiliser, metal ligand, proton acceptor
A	MSE235	metal ligand
A	CYS294	electrostatic stabiliser, proton acceptor
A	SER299	metal ligand

site_id	MCSA2
Number of Residues	5
Details	M-CSA 784

Chain	Residue	Details
B	PHE135	metal ligand
B	ALA137	electrostatic stabiliser, metal ligand, proton acceptor
B	MSE235	metal ligand
B	CYS294	electrostatic stabiliser, proton acceptor
B	SER299	metal ligand

site_id	MCSA3
Number of Residues	5
Details	M-CSA 784

Chain	Residue	Details
C	PHE135	metal ligand
C	ALA137	electrostatic stabiliser, metal ligand, proton acceptor
C	MSE235	metal ligand
C	CYS294	electrostatic stabiliser, proton acceptor
C	SER299	metal ligand

site_id	MCSA4
Number of Residues	5
Details	M-CSA 784

Chain	Residue	Details
D	PHE135	metal ligand
D	ALA137	electrostatic stabiliser, metal ligand, proton acceptor
D	MSE235	metal ligand
D	CYS294	electrostatic stabiliser, proton acceptor
D	SER299	metal ligand

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