PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1KEK
Asym. Unit
Info
Asym.Unit (426 KB)
Biol.Unit 1 (418 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE
Authors
:
E. Chabriere, X. Vernede, B. Guigliarelli, M. -H. Charon, E. C. Hatchikian, J. C. Fontecilla-Camps
Date
:
16 Nov 01 (Deposition) - 21 Dec 01 (Release) - 31 Mar 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Homodimer, 7 Domains, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Chabriere, X. Vernede, B. Guigliarelli, M. H. Charon, E. C. Hatchikian, J. C. Fontecilla-Camps
Crystal Structure Of The Free Radical Intermediate Of Pyruvate:Ferredoxin Oxidoreductase.
Science V. 294 2559 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 14)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: CARBON DIOXIDE (CO2a)
2b: CARBON DIOXIDE (CO2b)
3a: 2-ACETYL-THIAMINE DIPHOSPHATE (HTLa)
3b: 2-ACETYL-THIAMINE DIPHOSPHATE (HTLb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: IRON/SULFUR CLUSTER (SF4a)
5b: IRON/SULFUR CLUSTER (SF4b)
5c: IRON/SULFUR CLUSTER (SF4c)
5d: IRON/SULFUR CLUSTER (SF4d)
5e: IRON/SULFUR CLUSTER (SF4e)
5f: IRON/SULFUR CLUSTER (SF4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
CO2
2
Ligand/Ion
CARBON DIOXIDE
3
HTL
2
Ligand/Ion
2-ACETYL-THIAMINE DIPHOSPHATE
4
MG
2
Ligand/Ion
MAGNESIUM ION
5
SF4
6
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
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 , HTL A:2236 , HOH A:2375
BINDING SITE FOR RESIDUE MG A 2237
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 A 2238
03
AC3
SOFTWARE
ASP B:963 , THR B:991 , VAL B:993 , HTL B:3236 , HOH B:3382
BINDING SITE FOR RESIDUE MG B 3237
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 B 3238
05
AC5
SOFTWARE
TRP A:684 , CYS A:689 , ILE A:690 , CYS A:692 , ASN A:693 , CYS A:695 , CYS A:755 , PRO A:756 , LEU A:762
BINDING SITE FOR RESIDUE SF4 A 2233
06
AC6
SOFTWARE
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 A 2234
07
AC7
SOFTWARE
LYS A:459 , CYS A:812 , CYS A:815 , GLU A:817 , CYS A:840 , CYS A:1071 , ILE A:1072 , MET B:1203
BINDING SITE FOR RESIDUE SF4 A 2235
08
AC8
SOFTWARE
PRO A:29 , ILE A:30 , GLU A:64 , GLN A:88 , LEU A:92 , ARG A:114 , 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 , MG A:2237 , CO2 A:2240 , HOH A:2248 , HOH A:2264 , HOH A:2265 , HOH A:2375
BINDING SITE FOR RESIDUE HTL A 2236
09
AC9
SOFTWARE
THR A:31 , ARG A:114 , ASN A:996 , THR A:997 , HTL A:2236 , MET B:1202
BINDING SITE FOR RESIDUE CO2 A 2240
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 B 3233
11
BC2
SOFTWARE
CYS B:699 , PRO B:700 , ILE B:704 , CYS B:745 , MET B:746 , CYS B:748 , GLY B:749 , CYS B:751
BINDING SITE FOR RESIDUE SF4 B 3234
12
BC3
SOFTWARE
MET A:1203 , LYS B:459 , CYS B:812 , CYS B:815 , GLU B:817 , CYS B:840 , CYS B:1071 , ILE B:1072
BINDING SITE FOR RESIDUE SF4 B 3235
13
BC4
SOFTWARE
PRO B:29 , GLU B:64 , GLN B:88 , LEU B:92 , ARG B:114 , GLU B:817 , THR B:838 , GLY B:839 , CYS B:840 , PHE B:869 , GLU B:870 , 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:3237 , CO2 B:3240 , HOH B:3273 , HOH B:3308 , HOH B:3340 , HOH B:3382
BINDING SITE FOR RESIDUE HTL B 3236
14
BC5
SOFTWARE
MET A:1202 , ILE B:30 , THR B:31 , ARG B:114 , ASN B:996 , THR B:997 , HTL B:3236
BINDING SITE FOR RESIDUE CO2 B 3240
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
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
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
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_d1keka5 (A:669-785)
1b: SCOP_d1kekb5 (B:669-785)
2a: SCOP_d1keka4 (A:416-668)
2b: SCOP_d1kekb4 (B:416-668)
3a: SCOP_d1keka2 (A:786-1232)
3b: SCOP_d1kekb2 (B:786-1232)
4a: SCOP_d1keka1 (A:2-258)
4b: SCOP_d1kekb1 (B:2-258)
5a: SCOP_d1keka3 (A:259-415)
5b: SCOP_d1kekb3 (B:259-415)
View:
Select:
Label:
Classes
(
)
(
)
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
d1keka5
A:669-785
1b
d1kekb5
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
d1keka4
A:416-668
2b
d1kekb4
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
d1keka2
A:786-1232
3b
d1kekb2
B:786-1232
Family
:
PFOR Pyr module
(10)
Protein domain
:
Pyruvate-ferredoxin oxidoreductase, PFOR, domain I
(10)
Desulfovibrio africanus [TaxId: 873]
(10)
4a
d1keka1
A:2-258
4b
d1kekb1
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
d1keka3
A:259-415
5b
d1kekb3
B:259-415
[
close SCOP info
]
CATH Domains
(6, 14)
Info
all CATH domains
1a: CATH_1kekA05 (A:669-785)
1b: CATH_1kekB05 (B:669-785)
2a: CATH_1kekA03 (A:416-627)
2b: CATH_1kekB03 (B:416-627)
3a: CATH_1kekA02 (A:259-415)
3b: CATH_1kekB02 (B:259-415)
4a: CATH_1kekA01 (A:2-258)
4b: CATH_1kekA06 (A:786-1170)
4c: CATH_1kekB06 (B:786-1170)
4d: CATH_1kekB01 (B:2-258)
5a: CATH_1kekA04 (A:628-668)
5b: CATH_1kekB04 (B:628-668)
6a: CATH_1kekA07 (A:1171-1232)
6b: CATH_1kekB07 (B:1171-1232)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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
1kekA05
A:669-785
1b
1kekB05
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
1kekA03
A:416-627
2b
1kekB03
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
1kekA02
A:259-415
3b
1kekB02
B:259-415
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Desulfovibrio africanus. Organism_taxid: 873
(8)
4a
1kekA01
A:2-258
4b
1kekA06
A:786-1170
4c
1kekB06
B:786-1170
4d
1kekB01
B:2-258
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
1kekA04
A:628-668
5b
1kekB04
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
1kekA07
A:1171-1232
6b
1kekB07
B:1171-1232
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (426 KB)
Header - Asym.Unit
Biol.Unit 1 (418 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1KEK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help