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2C3O
Asym. Unit
Info
Asym.Unit (404 KB)
Biol.Unit 1 (394 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS
Authors
:
C. Cavazza, C. Contreras-Martel, L. Pieulle, E. Chabriere, E. C. Hatchikian, J. C. Fontecilla-Camps
Date
:
11 Oct 05 (Deposition) - 15 Feb 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Oxidoreductase, 4Fe-4S, Iron, Iron-Sulfur, Iron-Sulfur Cluster, Pyruvate Catabolism, Tpp-Dependent Enzyme, Metal-Binding, Electron Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Cavazza, C. Contreras-Martel, L. Pieulle, E. Chabriere, E. C. Hatchikian, J. C. Fontecilla-Camps
Flexibility Of Thiamine Diphosphate Revealed By Kinetic Crystallographic Studies Of The Reaction Of Pyruvate-Ferredoxin Oxidoreductase With Pyruvate.
Structure V. 14 217 2006
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 14)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: PYRUVIC ACID (PYRa)
3b: PYRUVIC ACID (PYRb)
4a: IRON/SULFUR CLUSTER (SF4a)
4b: IRON/SULFUR CLUSTER (SF4b)
4c: IRON/SULFUR CLUSTER (SF4c)
4d: IRON/SULFUR CLUSTER (SF4d)
4e: IRON/SULFUR CLUSTER (SF4e)
4f: IRON/SULFUR CLUSTER (SF4f)
5a: THIAMINE DIPHOSPHATE (TPPa)
5b: THIAMINE DIPHOSPHATE (TPPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
MG
2
Ligand/Ion
MAGNESIUM ION
3
PYR
2
Ligand/Ion
PYRUVIC ACID
4
SF4
6
Ligand/Ion
IRON/SULFUR CLUSTER
5
TPP
2
Ligand/Ion
THIAMINE DIPHOSPHATE
[
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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: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:963 , THR A:991 , VAL A:993 , HOH A:2209 , TPP A:2236
BINDING SITE FOR RESIDUE MG A2237
02
AC2
SOFTWARE
ASP A:983 , ASN A:985 , ALA A:1056 , GLU A:1057 , PHE A:1059 , GLY A:1061 , SER A:1063
BINDING SITE FOR RESIDUE CA A2238
03
AC3
SOFTWARE
ASP B:963 , THR B:991 , VAL B:993 , TPP B:2236 , HOH B:2255
BINDING SITE FOR RESIDUE MG B2237
04
AC4
SOFTWARE
ASP B:983 , ASN B:985 , ALA B:1056 , GLU B:1057 , PHE B:1059 , GLY B:1061 , SER B:1063
BINDING SITE FOR RESIDUE CA B2238
05
AC5
SOFTWARE
CYS A:689 , ILE A:690 , CYS A:692 , ASN A:693 , CYS A:695 , CYS A:755 , LEU A:762
BINDING SITE FOR RESIDUE SF4 A2233
06
AC6
SOFTWARE
PRO A:682 , CYS A:699 , ILE A:704 , CYS A:745 , MET A:746 , CYS A:748 , GLY A:749 , CYS A:751
BINDING SITE FOR RESIDUE SF4 A2234
07
AC7
SOFTWARE
LYS A:459 , CYS A:812 , CYS A:815 , GLU A:817 , CYS A:840 , TRP A:844 , CYS A:1071 , MET B:1203
BINDING SITE FOR RESIDUE SF4 A2235
08
AC8
SOFTWARE
PRO A:29 , ILE A:30 , GLU A:64 , GLN A:88 , LEU A:92 , GLU A:817 , THR A:838 , GLY A:839 , CYS A:840 , PHE A:869 , GLU A:870 , GLY A:962 , ASP A:963 , GLY A:964 , TRP A:965 , THR A:991 , VAL A:993 , TYR A:994 , SER A:995 , ASN A:996 , THR A:997 , HOH A:2179 , HOH A:2180 , HOH A:2190 , HOH A:2209 , MG A:2237 , PYR A:2239
BINDING SITE FOR RESIDUE TPP A2236
09
AC9
SOFTWARE
THR A:31 , ARG A:114 , ASN A:996 , THR A:997 , TPP A:2236 , MET B:1202
BINDING SITE FOR RESIDUE PYR A2239
10
BC1
SOFTWARE
TRP B:684 , CYS B:689 , ILE B:690 , CYS B:692 , ASN B:693 , CYS B:695 , CYS B:755 , PRO B:756 , ALA B:761 , LEU B:762
BINDING SITE FOR RESIDUE SF4 B2233
11
BC2
SOFTWARE
CYS B:699 , PRO B:700 , ALA B:703 , ILE B:704 , CYS B:745 , MET B:746 , CYS B:748 , GLY B:749 , CYS B:751
BINDING SITE FOR RESIDUE SF4 B2234
12
BC3
SOFTWARE
LYS B:459 , CYS B:812 , CYS B:815 , GLU B:817 , CYS B:840 , CYS B:1071
BINDING SITE FOR RESIDUE SF4 B2235
13
BC4
SOFTWARE
TYR B:28 , PRO B:29 , GLU B:64 , GLN B:88 , LEU B:92 , GLU B:817 , GLY B:839 , CYS B:840 , PHE B:869 , GLY B:962 , ASP B:963 , GLY B:964 , TRP B:965 , THR B:991 , VAL B:993 , TYR B:994 , SER B:995 , ASN B:996 , THR B:997 , MG B:2237 , PYR B:2239 , HOH B:2255 , HOH B:2307
BINDING SITE FOR RESIDUE TPP B2236
14
BC5
SOFTWARE
MET A:1202 , THR B:31 , ARG B:114 , ASN B:996 , THR B:997 , TPP B:2236
BINDING SITE FOR RESIDUE PYR B2239
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_FER_2 (A:680-709,B:680-709|A:736-767,B:73...)
2: 4FE4S_FER_1 (A:689-700,B:689-700|A:745-756,B:74...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
POR_DESAF
680-709
736-767
4
A:680-709
B:680-709
A:736-767
B:736-767
2
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
POR_DESAF
689-700
745-756
4
A:689-700
B:689-700
A:745-756
B:745-756
[
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]
Exons
(0, 0)
Info
All Exons
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(5, 10)
Info
All SCOP Domains
1a: SCOP_d2c3oa5 (A:669-785)
1b: SCOP_d2c3ob5 (B:669-785)
2a: SCOP_d2c3oa4 (A:416-668)
2b: SCOP_d2c3ob4 (B:416-668)
3a: SCOP_d2c3oa2 (A:786-1232)
3b: SCOP_d2c3ob2 (B:786-1232)
4a: SCOP_d2c3oa1 (A:2-258)
4b: SCOP_d2c3ob1 (B:2-258)
5a: SCOP_d2c3oa3 (A:259-415)
5b: SCOP_d2c3ob3 (B:259-415)
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
4Fe-4S ferredoxins
(143)
Family
:
Ferredoxin domains from multidomain proteins
(69)
Protein domain
:
Pyruvate-ferredoxin oxidoreductase, PFOR, domain V
(10)
Desulfovibrio africanus [TaxId: 873]
(10)
1a
d2c3oa5
A:669-785
1b
d2c3ob5
B:669-785
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
(10)
Superfamily
:
Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
(10)
Family
:
Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
(10)
Protein domain
:
Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
(10)
Desulfovibrio africanus [TaxId: 873]
(10)
2a
d2c3oa4
A:416-668
2b
d2c3ob4
B:416-668
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
PFOR PP module
(10)
Protein domain
:
Pyruvate-ferredoxin oxidoreductase, PFOR, domains VI
(10)
Desulfovibrio africanus [TaxId: 873]
(10)
3a
d2c3oa2
A:786-1232
3b
d2c3ob2
B:786-1232
Family
:
PFOR Pyr module
(10)
Protein domain
:
Pyruvate-ferredoxin oxidoreductase, PFOR, domain I
(10)
Desulfovibrio africanus [TaxId: 873]
(10)
4a
d2c3oa1
A:2-258
4b
d2c3ob1
B:2-258
Fold
:
TK C-terminal domain-like
(79)
Superfamily
:
TK C-terminal domain-like
(79)
Family
:
Pyruvate-ferredoxin oxidoreductase, PFOR, domain II
(10)
Protein domain
:
Pyruvate-ferredoxin oxidoreductase, PFOR, domain II
(10)
Desulfovibrio africanus [TaxId: 873]
(10)
5a
d2c3oa3
A:259-415
5b
d2c3ob3
B:259-415
[
close SCOP info
]
CATH Domains
(6, 14)
Info
all CATH domains
1a: CATH_2c3oA05 (A:669-785)
1b: CATH_2c3oB05 (B:669-785)
2a: CATH_2c3oA03 (A:416-627)
2b: CATH_2c3oB03 (B:416-627)
3a: CATH_2c3oA02 (A:259-415)
3b: CATH_2c3oB02 (B:259-415)
4a: CATH_2c3oA01 (A:2-258)
4b: CATH_2c3oB01 (B:2-258)
4c: CATH_2c3oA06 (A:786-1170)
4d: CATH_2c3oB06 (B:786-1170)
5a: CATH_2c3oA04 (A:628-668)
5b: CATH_2c3oB04 (B:628-668)
6a: CATH_2c3oA07 (A:1171-1232)
6b: CATH_2c3oB07 (B:1171-1232)
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)
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)
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)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.20, no name defined]
(120)
Desulfovibrio africanus. Organism_taxid: 873
(9)
1a
2c3oA05
A:669-785
1b
2c3oB05
B:669-785
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Pyruvate-ferredoxin Oxidoreductase; domain 3
(11)
Homologous Superfamily
:
Pyruvate-ferredoxin Oxidoreductase; domain 3
(11)
Desulfovibrio africanus. Organism_taxid: 873
(8)
2a
2c3oA03
A:416-627
2b
2c3oB03
B:416-627
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.920, no name defined]
(73)
Desulfovibrio africanus. Organism_taxid: 873
(8)
3a
2c3oA02
A:259-415
3b
2c3oB02
B:259-415
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Desulfovibrio africanus. Organism_taxid: 873
(8)
4a
2c3oA01
A:2-258
4b
2c3oB01
B:2-258
4c
2c3oA06
A:786-1170
4d
2c3oB06
B:786-1170
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Pyruvate-ferredoxin Oxidoreductase; domain 4
(10)
Homologous Superfamily
:
Pyruvate-ferredoxin Oxidoreductase; domain 4
(10)
Desulfovibrio africanus. Organism_taxid: 873
(8)
5a
2c3oA04
A:628-668
5b
2c3oB04
B:628-668
Topology
:
Pyruvate-ferredoxin Oxidoreductase; domain 7
(10)
Homologous Superfamily
:
Pyruvate-ferredoxin Oxidoreductase; domain 7
(10)
Desulfovibrio africanus. Organism_taxid: 873
(8)
6a
2c3oA07
A:1171-1232
6b
2c3oB07
B:1171-1232
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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