Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

9DB2

Class Ia ribonucleotide reductase with mechanism-based inhibitor N3CDP

This is a non-PDB format compatible entry.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003824	molecular_function	catalytic activity
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	0000166	molecular_function	nucleotide binding
B	0003824	molecular_function	catalytic activity
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	0005506	molecular_function	iron ion binding
C	0005515	molecular_function	protein binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
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	0046872	molecular_function	metal ion binding
D	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
D	0005506	molecular_function	iron ion binding
D	0005515	molecular_function	protein binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
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	0046872	molecular_function	metal ion binding

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
C	SER114-VAL130

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	ACT_SITE:

Chain	Residue	Details
C	TYR122
D	TYR122
B	ASN437
B	GLU441

site_id	SWS_FT_FI2
Number of Residues	12
Details	BINDING:

Chain	Residue	Details
C	ASP84
D	GLU204
D	GLU238
D	HIS241
C	GLU115
C	HIS118
C	GLU204
C	GLU238
C	HIS241
D	ASP84
D	GLU115
D	HIS118

site_id	SWS_FT_FI3
Number of Residues	8
Details	BINDING: BINDING => ECO:0000269\|PubMed:9309223, ECO:0007744\|PDB:3R1R

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

site_id	SWS_FT_FI4
Number of Residues	14
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
A	ASP232
A	ARG262
A	ARG269
A	ASN437
A	GLU441
A	GLU623
B	THR209
B	ASP232

site_id	SWS_FT_FI5
Number of Residues	4
Details	SITE: Important for hydrogen atom transfer

Chain	Residue	Details
A	CYS225
A	CYS462
B	CYS225
B	CYS462

site_id	SWS_FT_FI6
Number of Residues	4
Details	SITE: Important for electron transfer

Chain	Residue	Details
A	TYR730
A	TYR731
B	TYR730
B	TYR731

site_id	SWS_FT_FI7
Number of Residues	4
Details	SITE: Interacts with thioredoxin/glutaredoxin

Chain	Residue	Details
A	CYS754
A	CYS759
B	CYS754
B	CYS759

site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:18723842

Chain	Residue	Details
A	LYS283
B	LYS283

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	2
Details	M-CSA 918

Chain	Residue	Details
C	TYR122	pi-pi interaction, single electron relay
C	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
D	TYR122	pi-pi interaction, single electron relay
D	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

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		Validation report (PDF)