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3R1R
Biol. Unit 8
Info
Asym.Unit (368 KB)
Biol.Unit 1 (125 KB)
Biol.Unit 2 (125 KB)
Biol.Unit 3 (124 KB)
Biol.Unit 4 (717 KB)
Biol.Unit 5 (713 KB)
Biol.Unit 6 (715 KB)
Biol.Unit 7 (704 KB)
Biol.Unit 8 (703 KB)
Biol.Unit 9 (125 KB)
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(1)
Title
:
RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH AMPPNP OCCUPYING THE ACTIVITY 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,P (3x)
Biol. Unit 5: C,F (6x)
Biol. Unit 6: A,B,D,E (3x)
Biol. Unit 7: A,B,P (3x)
Biol. Unit 8: A,B (3x)
Biol. Unit 9: A,D (1x)
Keywords
:
Ribonucleotide Reductase, Deoxyribonucleotide Synthesis, Radical Chemistry, Allosteric Regulation, Specificity, Complex (Oxidoreductase/Peptide)
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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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
(for further references see the
PDB file header
)
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Hetero Components
(1, 6)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
1c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
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No.
Name
Count
Type
Full Name
1
ATP
6
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (UNKNOWN)
3: AC4 (SOFTWARE)
4: ACT (UNKNOWN)
5: AF2 (UNKNOWN)
6: AFF (UNKNOWN)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:9 , GLU A:15 , ARG A:16 , ILE A:17 , ASN A:18 , LYS A:21 , ILE A:22 , VAL A:25 , THR A:55 , HIS A:59 , LYS A:91
BINDING SITE FOR RESIDUE ATP 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
AC4
SOFTWARE
LYS B:9 , GLU B:15 , ARG B:16 , ILE B:17 , ASN B:18 , LYS B:21 , ILE B:22 , VAL B:25 , THR B:55 , HIS B:59 , LYS B:91
BINDING SITE FOR RESIDUE ATP B 762
4
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.
5
AF2
UNKNOWN
VAL B:7 , LYS B:9 , ARG B:10 , GLU B:15 , LYS B:21 , ILE B:22 , THR B:55 , ILE B:58 , HIS B:59 , HIS B:88 , LYS B:91
RESIDUES INVOLVED IN BINDING AMPPNP (ATP) AT THE ACTIVITY SITE. THE ACTIVITY SITE REGULATES THE ACTIVITY. EFFECTORS THAT CAN BIND ARE ATP (ACTIVATOR) OR DATP (INHIBITOR).
6
AFF
UNKNOWN
VAL A:7 , LYS A:9 , ARG A:10 , GLU A:15 , LYS A:21 , ILE A:22 , THR A:55 , ILE A:58 , HIS A:59 , HIS A:88 , LYS A:91
RESIDUES INVOLVED IN BINDING AMPPNP (ATP) AT THE ACTIVITY SITE. THE ACTIVITY SITE REGULATES THE ACTIVITY. EFFECTORS THAT CAN BIND ARE ATP (ACTIVATOR) OR DATP (INHIBITOR).
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: ATP_CONE (A:5-95,B:5-95)
2: RIBORED_LARGE (A:599-621,B:599-621)
;
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End label:
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
-
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d3r1ra1 (A:5-221)
1b: SCOP_d3r1rb1 (B:5-221)
1c: SCOP_d3r1rc1 (C:5-221)
2a: SCOP_d3r1ra2 (A:222-737)
2b: SCOP_d3r1rb2 (B:222-737)
2c: SCOP_d3r1rc2 (C:222-737)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
R1 subunit of ribonucleotide reductase, N-terminal domain
(13)
Superfamily
:
R1 subunit of ribonucleotide reductase, N-terminal domain
(13)
Family
:
R1 subunit of ribonucleotide reductase, N-terminal domain
(13)
Protein domain
:
R1 subunit of ribonucleotide reductase, N-terminal domain
(13)
Escherichia coli [TaxId: 562]
(8)
1a
d3r1ra1
A:5-221
1b
d3r1rb1
B:5-221
1c
d3r1rc1
C:5-221
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PFL-like glycyl radical enzymes
(32)
Superfamily
:
PFL-like glycyl radical enzymes
(32)
Family
:
R1 subunit of ribonucleotide reductase, C-terminal domain
(13)
Protein domain
:
R1 subunit of ribonucleotide reductase, C-terminal domain
(13)
Escherichia coli [TaxId: 562]
(8)
2a
d3r1ra2
A:222-737
2b
d3r1rb2
B:222-737
2c
d3r1rc2
C:222-737
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(3, 9)
Info
all PFAM domains
1a: PFAM_Ribonuc_red_lgC_3r1rC01 (C:222-732)
1b: PFAM_Ribonuc_red_lgC_3r1rC02 (C:222-732)
1c: PFAM_Ribonuc_red_lgC_3r1rC03 (C:222-732)
2a: PFAM_ATP_cone_3r1rC04 (C:5-92)
2b: PFAM_ATP_cone_3r1rC05 (C:5-92)
2c: PFAM_ATP_cone_3r1rC06 (C:5-92)
3a: PFAM_Ribonuc_red_lgN_3r1rC07 (C:141-220)
3b: PFAM_Ribonuc_red_lgN_3r1rC08 (C:141-220)
3c: PFAM_Ribonuc_red_lgN_3r1rC09 (C:141-220)
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)
Clan
:
PFL-like
(29)
Family
:
Ribonuc_red_lgC
(23)
Escherichia coli (strain K12)
(12)
1a
Ribonuc_red_lgC-3r1rC01
C:222-732
1b
Ribonuc_red_lgC-3r1rC02
C:222-732
1c
Ribonuc_red_lgC-3r1rC03
C:222-732
Clan
:
no clan defined [family: ATP-cone]
(16)
Family
:
ATP-cone
(16)
Escherichia coli (strain K12)
(12)
2a
ATP-cone-3r1rC04
C:5-92
2b
ATP-cone-3r1rC05
C:5-92
2c
ATP-cone-3r1rC06
C:5-92
Clan
:
no clan defined [family: Ribonuc_red_lgN]
(22)
Family
:
Ribonuc_red_lgN
(22)
Escherichia coli (strain K12)
(12)
3a
Ribonuc_red_lgN-3r1rC07
C:141-220
3b
Ribonuc_red_lgN-3r1rC08
C:141-220
3c
Ribonuc_red_lgN-3r1rC09
C:141-220
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Asym.Unit (368 KB)
Header - Asym.Unit
Biol.Unit 1 (125 KB)
Header - Biol.Unit 1
Biol.Unit 2 (125 KB)
Header - Biol.Unit 2
Biol.Unit 3 (124 KB)
Header - Biol.Unit 3
Biol.Unit 4 (717 KB)
Header - Biol.Unit 4
Biol.Unit 5 (713 KB)
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Biol.Unit 6 (715 KB)
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Biol.Unit 7 (704 KB)
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Biol.Unit 8 (703 KB)
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Biol.Unit 9 (125 KB)
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