Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5CNU

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to ADP and dGTP at 3.40 Angstroms resolution

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005829	cellular_component	cytosol
A	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
A	0006457	biological_process	protein folding
A	0009185	biological_process	ribonucleoside diphosphate metabolic process
A	0009263	biological_process	deoxyribonucleotide biosynthetic process
A	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
A	0015949	biological_process	nucleobase-containing small molecule interconversion
A	0016491	molecular_function	oxidoreductase activity
A	0042802	molecular_function	identical protein binding
A	0044183	molecular_function	protein folding chaperone
B	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005829	cellular_component	cytosol
B	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
B	0006457	biological_process	protein folding
B	0009185	biological_process	ribonucleoside diphosphate metabolic process
B	0009263	biological_process	deoxyribonucleotide biosynthetic process
B	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
B	0015949	biological_process	nucleobase-containing small molecule interconversion
B	0016491	molecular_function	oxidoreductase activity
B	0042802	molecular_function	identical protein binding
B	0044183	molecular_function	protein folding chaperone
C	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005829	cellular_component	cytosol
C	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
C	0006457	biological_process	protein folding
C	0009185	biological_process	ribonucleoside diphosphate metabolic process
C	0009263	biological_process	deoxyribonucleotide biosynthetic process
C	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
C	0015949	biological_process	nucleobase-containing small molecule interconversion
C	0016491	molecular_function	oxidoreductase activity
C	0042802	molecular_function	identical protein binding
C	0044183	molecular_function	protein folding chaperone
D	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005829	cellular_component	cytosol
D	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
D	0006457	biological_process	protein folding
D	0009185	biological_process	ribonucleoside diphosphate metabolic process
D	0009263	biological_process	deoxyribonucleotide biosynthetic process
D	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
D	0015949	biological_process	nucleobase-containing small molecule interconversion
D	0016491	molecular_function	oxidoreductase activity
D	0042802	molecular_function	identical protein binding
D	0044183	molecular_function	protein folding chaperone
E	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
E	0005506	molecular_function	iron ion binding
E	0005515	molecular_function	protein binding
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
E	0009185	biological_process	ribonucleoside diphosphate metabolic process
E	0009263	biological_process	deoxyribonucleotide biosynthetic process
E	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
E	0015949	biological_process	nucleobase-containing small molecule interconversion
E	0016491	molecular_function	oxidoreductase activity
E	0042802	molecular_function	identical protein binding
E	0046872	molecular_function	metal ion binding
F	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
F	0005506	molecular_function	iron ion binding
F	0005515	molecular_function	protein binding
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
F	0009185	biological_process	ribonucleoside diphosphate metabolic process
F	0009263	biological_process	deoxyribonucleotide biosynthetic process
F	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
F	0015949	biological_process	nucleobase-containing small molecule interconversion
F	0016491	molecular_function	oxidoreductase activity
F	0042802	molecular_function	identical protein binding
F	0046872	molecular_function	metal ion binding
G	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
G	0005506	molecular_function	iron ion binding
G	0005515	molecular_function	protein binding
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
G	0009185	biological_process	ribonucleoside diphosphate metabolic process
G	0009263	biological_process	deoxyribonucleotide biosynthetic process
G	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
G	0015949	biological_process	nucleobase-containing small molecule interconversion
G	0016491	molecular_function	oxidoreductase activity
G	0042802	molecular_function	identical protein binding
G	0046872	molecular_function	metal ion binding
H	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
H	0005506	molecular_function	iron ion binding
H	0005515	molecular_function	protein binding
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
H	0009185	biological_process	ribonucleoside diphosphate metabolic process
H	0009263	biological_process	deoxyribonucleotide biosynthetic process
H	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
H	0015949	biological_process	nucleobase-containing small molecule interconversion
H	0016491	molecular_function	oxidoreductase activity
H	0042802	molecular_function	identical protein binding
H	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	15
Details	binding site for residue DGT A 801

Chain	Residue
A	ASP232
A	HOH908
A	HOH910
A	HOH911
B	SER249
B	CYS292
B	GLN294
A	SER233
A	LEU234
A	ARG262
A	ILE268
A	ARG269
A	HIS275
A	THR276
A	MG802

site_id	AC2
Number of Residues	4
Details	binding site for residue MG A 802

Chain	Residue
A	DGT801
A	HOH908
A	HOH910
A	HOH911

site_id	AC3
Number of Residues	19
Details	binding site for residue ADP A 803

Chain	Residue
A	THR209
A	SER224
A	CYS225
A	ALA252
A	GLY253
A	ARG298
A	GLY299
A	GLY300
A	ASN437
A	CYS439
A	GLU441
A	LEU464
A	MET620
A	PRO621
A	SER622
A	GLU623
A	THR624
A	SER625
A	HOH902

site_id	AC4
Number of Residues	19
Details	binding site for residue DAT A 804

Chain	Residue
A	VAL7
A	LYS9
A	ARG10
A	GLU15
A	ARG16
A	ILE17
A	ASN18
A	LYS21
A	ILE22
A	VAL25
A	THR55
A	HIS59
A	PHE87
A	LYS91
A	MG805
A	HOH909
A	HOH912
A	HOH913
A	HOH914

site_id	AC5
Number of Residues	5
Details	binding site for residue MG A 805

Chain	Residue
A	DAT804
A	HOH909
A	HOH912
A	HOH913
A	HOH914

site_id	AC6
Number of Residues	20
Details	binding site for residue ADP B 801

Chain	Residue
B	PRO208
B	THR209
B	SER224
B	CYS225
B	ALA252
B	GLY253
B	ARG298
B	GLY299
B	GLY300
B	ASN437
B	CYS439
B	GLU441
B	LEU464
B	MET620
B	PRO621
B	SER622
B	GLU623
B	THR624
B	SER625
B	HOH904

site_id	AC7
Number of Residues	18
Details	binding site for residue DAT B 802

Chain	Residue
B	HOH921
B	LYS9
B	ARG10
B	GLU15
B	ARG16
B	ILE17
B	ASN18
B	LYS21
B	ILE22
B	VAL25
B	THR55
B	HIS59
B	ILE62
B	PHE87
B	MG803
B	HOH918
B	HOH919
B	HOH920

site_id	AC8
Number of Residues	5
Details	binding site for residue MG B 803

Chain	Residue
B	DAT802
B	HOH918
B	HOH919
B	HOH920
B	HOH921

site_id	AC9
Number of Residues	17
Details	binding site for residue DGT B 804

Chain	Residue
A	SER249
A	CYS292
A	GLN294
B	ASP232
B	SER233
B	LEU234
B	ARG262
B	ILE268
B	ARG269
B	HIS275
B	THR276
B	PHE281
B	MG805
B	HOH901
B	HOH915
B	HOH916
B	HOH917

site_id	AD1
Number of Residues	4
Details	binding site for residue MG B 805

Chain	Residue
B	DGT804
B	HOH915
B	HOH916
B	HOH917

site_id	AD2
Number of Residues	19
Details	binding site for residue ADP C 801

Chain	Residue
C	THR209
C	SER224
C	CYS225
C	ALA252
C	GLY253
C	ARG298
C	GLY299
C	GLY300
C	ASN437
C	CYS439
C	GLU441
C	LEU464
C	MET620
C	PRO621
C	SER622
C	GLU623
C	THR624
C	SER625
C	HOH901

site_id	AD3
Number of Residues	19
Details	binding site for residue DAT C 802

Chain	Residue
C	VAL7
C	LYS9
C	ARG10
C	GLU15
C	ARG16
C	ILE17
C	ASN18
C	LYS21
C	ILE22
C	VAL25
C	THR55
C	HIS59
C	PHE87
C	LYS91
C	MG803
C	HOH905
C	HOH907
C	HOH908
C	HOH909

site_id	AD4
Number of Residues	5
Details	binding site for residue MG C 803

Chain	Residue
C	DAT802
C	HOH905
C	HOH907
C	HOH908
C	HOH909

site_id	AD5
Number of Residues	17
Details	binding site for residue DGT C 804

Chain	Residue
C	ASP232
C	SER233
C	LEU234
C	ILE261
C	ARG262
C	ILE268
C	ARG269
C	HIS275
C	THR276
C	PHE281
C	MG805
C	HOH903
C	HOH904
C	HOH906
D	SER249
D	CYS292
D	GLN294

site_id	AD6
Number of Residues	4
Details	binding site for residue MG C 805

Chain	Residue
C	DGT804
C	HOH903
C	HOH904
C	HOH906

site_id	AD7
Number of Residues	20
Details	binding site for residue ADP D 801

Chain	Residue
D	PRO208
D	THR209
D	SER224
D	CYS225
D	ALA252
D	GLY253
D	ARG298
D	GLY299
D	GLY300
D	ASN437
D	CYS439
D	GLU441
D	LEU464
D	MET620
D	PRO621
D	SER622
D	GLU623
D	THR624
D	SER625
D	HOH904

site_id	AD8
Number of Residues	18
Details	binding site for residue DAT D 802

Chain	Residue
D	VAL7
D	LYS9
D	ARG10
D	GLU15
D	ARG16
D	ILE17
D	ASN18
D	LYS21
D	ILE22
D	VAL25
D	THR55
D	HIS59
D	PHE87
D	MG803
D	HOH903
D	HOH911
D	HOH912
D	HOH913

site_id	AD9
Number of Residues	5
Details	binding site for residue MG D 803

Chain	Residue
D	DAT802
D	HOH903
D	HOH911
D	HOH912
D	HOH913

site_id	AE1
Number of Residues	17
Details	binding site for residue DGT D 804

Chain	Residue
C	SER249
C	CYS292
C	GLN294
D	ASP232
D	SER233
D	LEU234
D	ILE261
D	ARG262
D	ILE268
D	ARG269
D	HIS275
D	THR276
D	PHE281
D	MG805
D	HOH908
D	HOH909
D	HOH910

site_id	AE2
Number of Residues	4
Details	binding site for residue MG D 805

Chain	Residue
D	DGT804
D	HOH908
D	HOH909
D	HOH910

site_id	AE3
Number of Residues	8
Details	binding site for residue FEO E 501

Chain	Residue
E	ASP84
E	GLU115
E	HIS118
E	GLU204
E	GLU238
E	HIS241
E	HOH601
E	HOH602

site_id	AE4
Number of Residues	8
Details	binding site for residue FEO F 501

Chain	Residue
F	ASP84
F	GLU115
F	HIS118
F	GLU204
F	GLU238
F	HIS241
F	HOH601
F	HOH602

site_id	AE5
Number of Residues	8
Details	binding site for residue FEO G 501

Chain	Residue
G	ASP84
G	GLU115
G	HIS118
G	GLU204
G	GLU238
G	HIS241
G	HOH601
G	HOH602

site_id	AE6
Number of Residues	8
Details	binding site for residue FEO H 501

Chain	Residue
H	ASP84
H	GLU115
H	HIS118
H	GLU204
H	GLU238
H	HIS241
H	HOH601
H	HOH602

Functional Information from PROSITE/UniProt

site_id	PS00089
Number of Residues	23
Details	RIBORED_LARGE Ribonucleotide reductase large subunit signature. WeaLresikthGLRNstlSAlmP

Chain	Residue	Details
A	TRP599-PRO621

site_id	PS00368
Number of Residues	17
Details	RIBORED_SMALL Ribonucleotide reductase small subunit signature. SEt.IHSrSYthIirnIV

Chain	Residue	Details
E	SER114-VAL130

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE:

Chain	Residue	Details
E	TYR122
F	TYR122
G	TYR122
H	TYR122
C	ASN437
C	GLU441
D	ASN437
D	GLU441

site_id	SWS_FT_FI2
Number of Residues	24
Details	BINDING:

Chain	Residue	Details
E	ASP84
F	GLU204
F	GLU238
F	HIS241
G	ASP84
G	GLU115
G	HIS118
G	GLU204
G	GLU238
G	HIS241
H	ASP84
E	GLU115
H	GLU115
H	HIS118
H	GLU204
H	GLU238
H	HIS241
E	HIS118
E	GLU204
E	GLU238
E	HIS241
F	ASP84
F	GLU115
F	HIS118

site_id	SWS_FT_FI3
Number of Residues	16
Details	BINDING: BINDING => ECO:0000269\|PubMed:9309223, ECO:0007744\|PDB:3R1R

Chain	Residue	Details
A	LYS9
C	GLU15
C	THR55
C	LYS91
D	LYS9
D	GLU15
D	THR55
D	LYS91
A	GLU15
A	THR55
A	LYS91
B	LYS9
B	GLU15
B	THR55
B	LYS91
C	LYS9

site_id	SWS_FT_FI4
Number of Residues	28
Details	BINDING: BINDING => ECO:0000269\|PubMed:9309223, ECO:0007744\|PDB:4R1R

Chain	Residue	Details
A	THR209
B	ARG262
B	ARG269
B	ASN437
B	GLU441
B	GLU623
C	THR209
C	ASP232
C	ARG262
C	ARG269
C	ASN437
A	ASP232
C	GLU441
C	GLU623
D	THR209
D	ASP232
D	ARG262
D	ARG269
D	ASN437
D	GLU441
D	GLU623
A	ARG262
A	ARG269
A	ASN437
A	GLU441
A	GLU623
B	THR209
B	ASP232

site_id	SWS_FT_FI5
Number of Residues	8
Details	SITE: Important for hydrogen atom transfer

Chain	Residue	Details
A	CYS225
A	CYS462
B	CYS225
B	CYS462
C	CYS225
C	CYS462
D	CYS225
D	CYS462

site_id	SWS_FT_FI6
Number of Residues	8
Details	SITE: Important for electron transfer

Chain	Residue	Details
A	TYR730
A	TYR731
B	TYR730
B	TYR731
C	TYR730
C	TYR731
D	TYR730
D	TYR731

site_id	SWS_FT_FI7
Number of Residues	8
Details	SITE: Interacts with thioredoxin/glutaredoxin

Chain	Residue	Details
A	CYS754
A	CYS759
B	CYS754
B	CYS759
C	CYS754
C	CYS759
D	CYS754
D	CYS759

site_id	SWS_FT_FI8
Number of Residues	4
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:18723842

Chain	Residue	Details
A	LYS283
B	LYS283
C	LYS283
D	LYS283

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	2
Details	M-CSA 918

Chain	Residue	Details
E	TYR122	pi-pi interaction, single electron relay
E	ASP237
A	CYS439	hydrogen radical acceptor, hydrogen radical donor, single electron acceptor
A	GLU441	proton acceptor
A	CYS462
A	TYR730	pi-pi interaction, single electron relay
A	TYR731	pi-pi interaction, single electron relay

site_id	MCSA2
Number of Residues	2
Details	M-CSA 918

Chain	Residue	Details
F	TYR122	pi-pi interaction, single electron relay
F	ASP237
B	CYS439	hydrogen radical acceptor, hydrogen radical donor, single electron acceptor
B	GLU441	proton acceptor
B	CYS462
B	TYR730	pi-pi interaction, single electron relay
B	TYR731	pi-pi interaction, single electron relay

site_id	MCSA3
Number of Residues	2
Details	M-CSA 918

Chain	Residue	Details
G	TYR122	pi-pi interaction, single electron relay
G	ASP237
C	CYS439	hydrogen radical acceptor, hydrogen radical donor, single electron acceptor
C	GLU441	proton acceptor
C	CYS462
C	TYR730	pi-pi interaction, single electron relay
C	TYR731	pi-pi interaction, single electron relay

site_id	MCSA4
Number of Residues	2
Details	M-CSA 918

Chain	Residue	Details
H	TYR122	pi-pi interaction, single electron relay
H	ASP237
D	CYS439	hydrogen radical acceptor, hydrogen radical donor, single electron acceptor
D	GLU441	proton acceptor
D	CYS462
D	TYR730	pi-pi interaction, single electron relay
D	TYR731	pi-pi interaction, single electron relay

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