2R1R - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Biological Unit 7 (Jmol Viewer)

Biological Unit 8 (Jmol Viewer)

Title :   RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH DTTP OCCUPYING THE SPECIFICITY SITE FROM ESCHERICHIA COLI

Authors :   M. Eriksson, H. Eklund

Date :   21 Jul 97 (Deposition) - 28 Jan 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B,C,D,E,F,P
Biol. Unit 1: A,D,P  (1x)
Biol. Unit 2: B,E  (1x)
Biol. Unit 3: C,F  (1x)
Biol. Unit 4: A,B,D,E  (3x)
Biol. Unit 5: C,F  (6x)
Biol. Unit 6: A,B,D,E  (1x)
Biol. Unit 7: C,F  (2x)
Biol. Unit 8: A,D  (1x)

Keywords :   Ribonucleotide Reductase, Deoxyribonucleotide Synthesis, Radical Chemistry, Allosteric Regulation, Specificity, Complex (Oxidoreductase/Peptide) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Eriksson, U. Uhlin, S. Ramaswamy, M. Ekberg, K. Regnstrom, B. M. Sjoberg, H. Eklund
Binding Of Allosteric Effectors To Ribonucleotide Reductase Protein R1: Reduction Of Active-Site Cysteines Promotes Substrate Binding.
Structure V. 5 1077 1997
PubMed-ID: 9309223 | Reference-DOI: 10.1016/S0969-2126(97)00259-1
(for further references see the PDB file header)

Molecule 1 - RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
	Chains	:	A, B, C
	EC Number	:	1.17.4.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	NRDA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
	Chains	:	D, E, F, P
	Engineered	:	YES
	Fragment	:	C-TERMINAL PORTION, 20 RESIDUES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4	5	6	7
Asymmetric Unit	:	A	B	C	D	E	F	P
Biological Unit 1 (1x)	:	A			D			P
Biological Unit 2 (1x)	:		B			E
Biological Unit 3 (1x)	:			C			F
Biological Unit 4 (3x)	:	A	B		D	E
Biological Unit 5 (6x)	:			C			F
Biological Unit 6 (1x)	:	A	B		D	E
Biological Unit 7 (2x)	:			C			F
Biological Unit 8 (1x)	:	A			D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	TTP	3	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	TTP	1	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	TTP	1	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	TTP	1	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Biological Unit 4 (1, 6)

No.	Name	Count	Type	Full Name
1	TTP	6	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Biological Unit 5 (1, 6)

No.	Name	Count	Type	Full Name
1	TTP	6	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Biological Unit 6 (1, 2)

No.	Name	Count	Type	Full Name
1	TTP	2	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Biological Unit 7 (1, 2)

No.	Name	Count	Type	Full Name
1	TTP	2	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Biological Unit 8 (1, 1)

No.	Name	Count	Type	Full Name
1	TTP	1	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:232 , SER A:233 , LEU A:234 , ARG A:262 , ILE A:268 , ARG A:269 , HIS A:275 , SER B:249	BINDING SITE FOR RESIDUE TTP A 762
2	AC2	UNKNOWN	CYS B:225 , CYS B:462 , CYS B:439 , ASN B:437 , GLU B:441	ACTIVE SITE, THE REDOX CENTER, CYS B 225 AND CYS B 462, IN THE OXIDIZED FORM.
3	AC3	UNKNOWN	CYS C:225 , CYS C:462 , CYS C:439 , ASN C:437 , GLU C:441	ACTIVE SITE, THE REDOX CENTER, CYS C 225 AND CYS C 462, IN THE OXIDIZED FORM.
4	AC4	SOFTWARE	SER A:249 , ASP B:232 , SER B:233 , LEU B:234 , ARG B:262 , ILE B:268 , ARG B:269 , HIS B:275	BINDING SITE FOR RESIDUE TTP B 762
5	AC5	SOFTWARE	ASP C:232 , SER C:233 , LEU C:234 , SER C:249 , ARG C:262 , ILE C:268 , ARG C:269 , HIS C:275	BINDING SITE FOR RESIDUE TTP C 762
6	ACT	UNKNOWN	CYS A:225 , CYS A:462 , CYS A:439 , ASN A:437 , GLU A:441	ACTIVE SITE, THE REDOX CENTER, CYS A 225 AND CYS A 462, IN THE OXIDIZED FORM.
7	SE2	UNKNOWN	ASP B:232 , LEU B:234 , ARG B:262 , ILE B:268 , HIS B:275 , PHE B:281 , CYS B:292	RESIDUES INVOLVED IN BINDING DTTP AT THE SPECIFICITY SITE THE SPECIFICITY SITE REGULATES THE SUBSTRATE SPECIFICITY. OTHER EFFECTORS THAT CAN BIND ARE DGTP, DATP AND ATP.
8	SE3	UNKNOWN	ASP C:232 , LEU C:234 , ARG C:262 , ILE C:268 , HIS C:275 , PHE C:281 , CYS C:292	RESIDUES INVOLVED IN BINDING DTTP AT THE SPECIFICITY SITE THE SPECIFICITY SITE REGULATES THE SUBSTRATE SPECIFICITY. OTHER EFFECTORS THAT CAN BIND ARE DGTP, DATP AND ATP.
9	SEC	UNKNOWN	ASP A:232 , LEU A:234 , ARG A:262 , ILE A:268 , HIS A:275 , PHE A:281 , CYS A:292	RESIDUES INVOLVED IN BINDING DTTP AT THE SPECIFICITY SITE THE SPECIFICITY SITE REGULATES THE SUBSTRATE SPECIFICITY. OTHER EFFECTORS THAT CAN BIND ARE DGTP, DATP AND ATP.

Asymmetric Unit

No.	Residues
1	A:225	-	A:462
2	B:225	-	B:462
3	C:225	-	C:462

(no "Cis Peptide Bond" information available for 2R1R)

(no "SAP(SNP)/Variant" information available for 2R1R)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ATP_CONE	PS51161	ATP-cone domain profile.	RIR1_ECOLI	5-95	3	A:5-95 B:5-95 C:5-95
2	RIBORED_LARGE	PS00089	Ribonucleotide reductase large subunit signature.	RIR1_ECOLI	599-621	3	A:599-621 B:599-621 C:599-621

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ATP_CONE	PS51161	ATP-cone domain profile.	RIR1_ECOLI	5-95	1	A:5-95 - -
2	RIBORED_LARGE	PS00089	Ribonucleotide reductase large subunit signature.	RIR1_ECOLI	599-621	1	A:599-621 - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ATP_CONE	PS51161	ATP-cone domain profile.	RIR1_ECOLI	5-95	1	- B:5-95 -
2	RIBORED_LARGE	PS00089	Ribonucleotide reductase large subunit signature.	RIR1_ECOLI	599-621	1	- B:599-621 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ATP_CONE	PS51161	ATP-cone domain profile.	RIR1_ECOLI	5-95	1	- - C:5-95
2	RIBORED_LARGE	PS00089	Ribonucleotide reductase large subunit signature.	RIR1_ECOLI	599-621	1	- - C:599-621

Biological Unit 4 (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ATP_CONE	PS51161	ATP-cone domain profile.	RIR1_ECOLI	5-95	6	A:5-95 B:5-95 -
2	RIBORED_LARGE	PS00089	Ribonucleotide reductase large subunit signature.	RIR1_ECOLI	599-621	6	A:599-621 B:599-621 -

Biological Unit 5 (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ATP_CONE	PS51161	ATP-cone domain profile.	RIR1_ECOLI	5-95	6	- - C:5-95
2	RIBORED_LARGE	PS00089	Ribonucleotide reductase large subunit signature.	RIR1_ECOLI	599-621	6	- - C:599-621

Biological Unit 6 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ATP_CONE	PS51161	ATP-cone domain profile.	RIR1_ECOLI	5-95	2	A:5-95 B:5-95 -
2	RIBORED_LARGE	PS00089	Ribonucleotide reductase large subunit signature.	RIR1_ECOLI	599-621	2	A:599-621 B:599-621 -

Biological Unit 7 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ATP_CONE	PS51161	ATP-cone domain profile.	RIR1_ECOLI	5-95	2	- - C:5-95
2	RIBORED_LARGE	PS00089	Ribonucleotide reductase large subunit signature.	RIR1_ECOLI	599-621	2	- - C:599-621

Biological Unit 8 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ATP_CONE	PS51161	ATP-cone domain profile.	RIR1_ECOLI	5-95	1	A:5-95 - -
2	RIBORED_LARGE	PS00089	Ribonucleotide reductase large subunit signature.	RIR1_ECOLI	599-621	1	A:599-621 - -

(no "Exon" information available for 2R1R)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:733
 aligned with RIR1_ECOLI | P00452 from UniProtKB/Swiss-Prot  Length:761

    Alignment length:733
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734   
           RIR1_ECOLI     5 LLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRDG 737
               SCOP domains d2r1ra1 A:5-221 R1 subunit of ribonucleotide reductase, N-terminal domain                                                                                                                                                d2r1ra2 A:222-737 R1 subunit of ribonucleotide reductase, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee..hhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.....hhhhhh..hhhhhhhhh...hhhhhh..hhhhhhhhhh..............hhhhhhhhhhhh........hhhhhhhhhhhhh...eee.hhhhhh..........eeeee....hhhhhhhhhhhhhhhhh..eeeee....................hhhhhhhhhhhh............eeeeee.....hhhh.........hhh.....eeeeee.hhhhhhhhh..eeeee.hhh...hhhhhhh.hhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhh..eeeeehhhhhh........................................eeeeee......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh..eeeeee.hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhh..hhh...hhhh..hhhhh.........hhhhhhhhhhh..............hhhhh.............eeeee....eeeee...hhhh......hhh....hhhhhhhhhhhhh........eee.hhh.hhh...hhhhhhhhhhhhh........eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ATP_CONE  PDB: A:5-95 UniProt: 5-95                                                        -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r1r A   5 LLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRDG 737
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734

Chain B from PDB  Type:PROTEIN  Length:733
 aligned with RIR1_ECOLI | P00452 from UniProtKB/Swiss-Prot  Length:761

    Alignment length:733
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734   
           RIR1_ECOLI     5 LLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRDG 737
               SCOP domains d2r1rb1 B:5-221 R1 subunit of ribonucleotide reductase, N-terminal domain                                                                                                                                                d2r1rb2 B:222-737 R1 subunit of ribonucleotide reductase, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee..hhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.....hhhhhh..hhhhhhhhh...hhhhhh..hhhhhhhhhh..............hhhhhhhhhhhh........hhhhhhhhhhhhh...eee.hhhhhh..........eeeee....hhhhhhhhhhhhhhhhh..eeeee....................hhhhhhhhhhhh............eeeeee.....hhhh.........hhh.....eeeeee.hhhhhhhhh..eeeee.hhh...hhhhhhh.hhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhh..eeeeehhhhhh........................................eeeeee......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh..eeeeee.hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhh..hhh...hhhh..hhhhh.........hhhhhhhhhhh..............hhhhh.............eeeee....eeeee...hhhh......hhh....hhhhhhhhhhhhh........eee.hhh.hhh...hhhhhhhhhhhhh........eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ATP_CONE  PDB: B:5-95 UniProt: 5-95                                                        -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r1r B   5 LLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRDG 737
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734

Chain C from PDB  Type:PROTEIN  Length:733
 aligned with RIR1_ECOLI | P00452 from UniProtKB/Swiss-Prot  Length:761

    Alignment length:733
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734   
           RIR1_ECOLI     5 LLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRDG 737
               SCOP domains d2r1rc1 C:5-221 R1 subunit of ribonucleotide reductase, N-terminal domain                                                                                                                                                d2r1rc2 C:222-737 R1 subunit of ribonucleotide reductase, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ATP-cone-2r1rC04 C:5-92                                                                 ------------------------------------------------Ribonuc_red_lgN-2r1rC07 C:141-220                                               -Ribonuc_red_lgC-2r1rC01 C:222-732                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ----- Pfam domains (1)
           Pfam domains (2) ATP-cone-2r1rC05 C:5-92                                                                 ------------------------------------------------Ribonuc_red_lgN-2r1rC08 C:141-220                                               -Ribonuc_red_lgC-2r1rC02 C:222-732                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ----- Pfam domains (2)
           Pfam domains (3) ATP-cone-2r1rC06 C:5-92                                                                 ------------------------------------------------Ribonuc_red_lgN-2r1rC09 C:141-220                                               -Ribonuc_red_lgC-2r1rC03 C:222-732                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ----- Pfam domains (3)
         Sec.struct. author .eee.....eee..hhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.....hhhhhh..hhhhhhhhh...hhhhhh..hhhhhhhhhh..............hhhhhhhhhhhh........hhhhhhhhhhhhh...eee.hhhhhh..........eeeee....hhhhhhhhhhhhhhhhh..eeeee....................hhhhhhhhhhhh............eeeeee.....hhhh.........hhh.....eeeeee.hhhhhhhhh..eeeee.hhh...hhhhhhh.hhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhh..eeeeehhhhhh........................................eeeeee......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh..eeeeee.hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhh..hhh...hhhh..hhhhh.........hhhhhhhhhhh..............hhhhh.............eeeee....eeeee...hhhh......hhh....hhhhhhhhhhhhh........eee.hhh.hhh...hhhhhhhhhhhhh........eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ATP_CONE  PDB: C:5-95 UniProt: 5-95                                                        -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r1r C   5 LLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRDG 737
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734

Chain D from PDB  Type:PROTEIN  Length:13
 aligned with RIR2_ECOLI | P69924 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:13
                                   373   
           RIR2_ECOLI   364 SEVDTDDLSNFQL 376
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ....hhhh..... Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 2r1r D 363 SEVDTDDLSNFQL 375
                                   372

Chain E from PDB  Type:PROTEIN  Length:13
 aligned with RIR2_ECOLI | P69924 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:13
                                   373   
           RIR2_ECOLI   364 SEVDTDDLSNFQL 376
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ....hhhh..... Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 2r1r E 363 SEVDTDDLSNFQL 375
                                   372

Chain F from PDB  Type:PROTEIN  Length:13
 aligned with RIR2_ECOLI | P69924 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:13
                                   373   
           RIR2_ECOLI   364 SEVDTDDLSNFQL 376
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ....hhhh..... Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 2r1r F 363 SEVDTDDLSNFQL 375
                                   372

Chain P from PDB  Type:PROTEIN  Length:4
 aligned with RIR2_ECOLI | P69924 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:4
           RIR2_ECOLI   357 YLVG 360
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2r1r P   1 YLVG   4

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "CATH Domain" information available for 2R1R)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (RIR1_ECOLI | P00452)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0004748	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor	Catalysis of the reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0009263	deoxyribonucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0015949	nucleobase-containing small molecule interconversion	The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005971	ribonucleoside-diphosphate reductase complex	An enzyme complex composed of 2-4 or more subunits, which usually contains nonheme iron and requires ATP for catalysis. Catalyzes the formation of 2'-deoxyribonucleoside diphosphate from ribonucleoside diphosphate, using either thioredoxin disulfide or glutaredoxin disulfide as an acceptor.

Chain D,E,F,P (RIR2_ECOLI | P69924)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0004748	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor	Catalysis of the reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0009186	deoxyribonucleoside diphosphate metabolic process	The chemical reactions and pathways involving a deoxyribonucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with diphosphate on the sugar.
	GO:0009263	deoxyribonucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0015949	nucleobase-containing small molecule interconversion	The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005971	ribonucleoside-diphosphate reductase complex	An enzyme complex composed of 2-4 or more subunits, which usually contains nonheme iron and requires ATP for catalysis. Catalyzes the formation of 2'-deoxyribonucleoside diphosphate from ribonucleoside diphosphate, using either thioredoxin disulfide or glutaredoxin disulfide as an acceptor.

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(no "Related Entries Specified in the PDB File" available for 2R1R)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (9, 9)

SS Bonds (3, 3)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 6)

Exons (0, 0)

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