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1PFR
Asym. Unit
Info
Asym.Unit (124 KB)
Biol.Unit 1 (119 KB)
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(1)
Title
:
RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA CHAIN
Authors
:
D. T. Logan, X. D. Su, A. Aberg, K. Regnstrom, J. Hajdu, H. Eklund, P. Nordlund
Date
:
03 Dec 96 (Deposition) - 12 Mar 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Reductase, Oxidoreductase, Dna Replication, Iron, Acting On Ribose 2'-Oh
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. T. Logan, X. D. Su, A. Aberg, K. Regnstrom, J. Hajdu, H. Eklund, P. Nordlund
Crystal Structure Of Reduced Protein R2 Of Ribonucleotide Reductase: The Structural Basis For Oxygen Activation At A Dinuclear Iron Site.
Structure V. 4 1053 1996
(for further references see the
PDB file header
)
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: FE (III) ION (FEa)
1b: FE (III) ION (FEb)
1c: FE (III) ION (FEc)
1d: FE (III) ION (FEd)
2a: MERCURY (II) ION (HGa)
2b: MERCURY (II) ION (HGb)
2c: MERCURY (II) ION (HGc)
2d: MERCURY (II) ION (HGd)
2e: MERCURY (II) ION (HGe)
2f: MERCURY (II) ION (HGf)
2g: MERCURY (II) ION (HGg)
2h: MERCURY (II) ION (HGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE
4
Ligand/Ion
FE (III) ION
2
HG
8
Ligand/Ion
MERCURY (II) ION
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Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: FE1 (UNKNOWN)
14: FE2 (UNKNOWN)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:84 , GLU A:115 , HIS A:118 , GLU A:238
BINDING SITE FOR RESIDUE FE A 501
02
AC2
SOFTWARE
GLU A:115 , GLU A:204 , GLU A:238 , HIS A:241
BINDING SITE FOR RESIDUE FE A 502
03
AC3
SOFTWARE
TYR A:156 , TYR A:157 , CYS A:196 , VAL A:200 , HG A:603 , HOH A:612
BINDING SITE FOR RESIDUE HG A 601
04
AC4
SOFTWARE
TYR A:194 , MET A:198 , ALA A:265 , CYS A:272 , HOH A:667
BINDING SITE FOR RESIDUE HG A 602
05
AC5
SOFTWARE
TYR A:157 , CYS A:196 , LEU A:197 , VAL A:200 , HG A:601
BINDING SITE FOR RESIDUE HG A 603
06
AC6
SOFTWARE
CYS A:268 , HOH A:695
BINDING SITE FOR RESIDUE HG A 604
07
AC7
SOFTWARE
ASP B:84 , GLU B:115 , HIS B:118 , GLU B:238 , FE B:504
BINDING SITE FOR RESIDUE FE B 503
08
AC8
SOFTWARE
GLU B:115 , GLU B:204 , GLU B:238 , HIS B:241 , FE B:503 , HOH B:663
BINDING SITE FOR RESIDUE FE B 504
09
AC9
SOFTWARE
TYR B:156 , TYR B:157 , CYS B:196 , VAL B:200 , HG B:606 , HOH B:617
BINDING SITE FOR RESIDUE HG B 605
10
BC1
SOFTWARE
TYR B:157 , CYS B:196 , VAL B:200 , HG B:605
BINDING SITE FOR RESIDUE HG B 606
11
BC2
SOFTWARE
TYR B:194 , CYS B:268 , CYS B:272
BINDING SITE FOR RESIDUE HG B 607
12
BC3
SOFTWARE
ILE B:72 , CYS B:214 , MET B:296
BINDING SITE FOR RESIDUE HG B 608
13
FE1
UNKNOWN
ASP A:84 , GLU A:115 , HIS A:118 , GLU A:204 , GLU A:238 , HIS A:241
DIFERROUS IRON CENTER IN SUBUNIT A.
14
FE2
UNKNOWN
ASP B:84 , GLU B:115 , HIS B:118 , GLU B:204 , GLU B:238 , HIS B:241
DIFERROUS IRON CENTER IN SUBUNIT B.
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: RIBORED_SMALL (A:114-130,B:114-130)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBORED_SMALL
PS00368
Ribonucleotide reductase small subunit signature.
RIR2_ECOLI
115-131
2
A:114-130
B:114-130
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1pfra_ (A:)
1b: SCOP_d1pfrb_ (B:)
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Protein Domains
(
)
(
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Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ribonucleotide reductase-like
(185)
Protein domain
:
Ribonucleotide reductase R2
(45)
Escherichia coli [TaxId: 562]
(24)
1a
d1pfra_
A:
1b
d1pfrb_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1pfrA00 (A:1-340)
1b: CATH_1pfrB00 (B:1-340)
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Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Ribonucleotide Reductase, subunit A
(86)
Homologous Superfamily
:
Ribonucleotide Reductase, subunit A
(86)
Escherichia coli. Organism_taxid: 562.
(9)
1a
1pfrA00
A:1-340
1b
1pfrB00
B:1-340
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Ribonuc_red_sm_1pfrB01 (B:181-335)
1b: PFAM_Ribonuc_red_sm_1pfrB02 (B:181-335)
1c: PFAM_Ribonuc_red_sm_1pfrB03 (B:181-335)
1d: PFAM_Ribonuc_red_sm_1pfrB04 (B:181-335)
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Clan
:
Ferritin
(185)
Family
:
Ribonuc_red_sm
(41)
Escherichia coli (strain K12)
(22)
1a
Ribonuc_red_sm-1pfrB01
B:181-335
1b
Ribonuc_red_sm-1pfrB02
B:181-335
1c
Ribonuc_red_sm-1pfrB03
B:181-335
1d
Ribonuc_red_sm-1pfrB04
B:181-335
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Asymmetric Unit 1
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Asym.Unit (124 KB)
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