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.
3P4Q
Asym. Unit
Info
Asym.Unit (722 KB)
Biol.Unit 1 (350 KB)
Biol.Unit 2 (364 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 MENAQUINOL:OXIDOREDUCTASE IN COMPLEX WITH OXALOACETATE
Authors
:
T. M. Tomasiak, T. L. Archuleta, J. Andrell, C. Luna-Chavez, T. A. Davis M. Sarwar, A. J. Ham, W. H. Mcdonald, V. Yankowskaya, H. A. Stern, J. N. J E. Maklashina, G. Cecchini, T. M. Iverson
Date
:
06 Oct 10 (Deposition) - 08 Dec 10 (Release) - 16 Mar 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.35
Chains
:
Asym. Unit : A,B,C,D,M,N,O,P
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: M,N,O,P (1x)
Keywords
:
Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. M. Tomasiak, T. L. Archuleta, J. Andrell, C. Luna-Chavez, T. A. Davis, M. Sarwar, A. J. Ham, W. H. Mcdonald, V. Yankovskaya, H. A. Stern, J. N. Johnston, E. Maklashina, G. Cecchini, T. M. Iverson
Geometric Restraint Drives On- And Off-Pathway Catalysis By The Escherichia Coli Menaquinol:Fumarate Reductase.
J. Biol. Chem. V. 286 3047 2011
[
close entry info
]
Hetero Components
(5, 10)
Info
All Hetero Components
1a: FE3-S4 CLUSTER (F3Sa)
1b: FE3-S4 CLUSTER (F3Sb)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
4a: OXALOACETATE ION (OAAa)
4b: OXALOACETATE ION (OAAb)
5a: IRON/SULFUR CLUSTER (SF4a)
5b: IRON/SULFUR CLUSTER (SF4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
F3S
2
Ligand/Ion
FE3-S4 CLUSTER
2
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
OAA
2
Ligand/Ion
OXALOACETATE ION
5
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:11 , ALA A:12 , GLY A:13 , GLY A:14 , ALA A:15 , SER A:36 , LYS A:37 , VAL A:38 , SER A:43 , HIS A:44 , THR A:45 , ALA A:48 , GLY A:50 , GLY A:51 , HIS A:155 , PHE A:156 , VAL A:157 , ALA A:191 , THR A:192 , GLY A:193 , THR A:203 , ASN A:204 , ASP A:211 , LEU A:242 , HIS A:355 , TYR A:356 , GLY A:378 , GLU A:379 , ARG A:390 , SER A:393 , ASN A:394 , SER A:395 , LEU A:396 , LEU A:399 , OAA A:702
BINDING SITE FOR RESIDUE FAD A 601
02
AC2
SOFTWARE
GLY A:50 , PHE A:116 , HIS A:232 , LEU A:242 , THR A:244 , GLU A:245 , HIS A:355 , ARG A:390 , GLY A:392 , SER A:393 , FAD A:601
BINDING SITE FOR RESIDUE OAA A 702
03
AC3
SOFTWARE
SER B:56 , CYS B:57 , ARG B:58 , CYS B:62 , GLY B:63 , SER B:64 , CYS B:65 , CYS B:77
BINDING SITE FOR RESIDUE FES B 244
04
AC4
SOFTWARE
CYS B:158 , GLN B:160 , CYS B:204 , THR B:205 , PHE B:206 , VAL B:207 , GLY B:208 , TYR B:209 , CYS B:210 , ILE B:224
BINDING SITE FOR RESIDUE F3S B 245
05
AC5
SOFTWARE
CYS B:148 , ILE B:149 , CYS B:151 , GLY B:152 , CYS B:154 , CYS B:214
BINDING SITE FOR RESIDUE SF4 B 246
06
AC6
SOFTWARE
GLY M:11 , ALA M:12 , GLY M:13 , GLY M:14 , ILE M:35 , SER M:36 , LYS M:37 , SER M:43 , HIS M:44 , THR M:45 , ALA M:47 , ALA M:48 , GLY M:50 , GLY M:51 , HIS M:155 , PHE M:156 , VAL M:157 , ALA M:191 , THR M:192 , GLY M:193 , THR M:203 , ASN M:204 , ILE M:207 , LEU M:242 , HIS M:355 , TYR M:356 , GLU M:379 , SER M:393 , SER M:395 , LEU M:396 , LEU M:399 , OAA M:802
BINDING SITE FOR RESIDUE FAD M 601
07
AC7
SOFTWARE
PHE M:116 , HIS M:232 , THR M:244 , GLU M:245 , ARG M:287 , HIS M:355 , ARG M:390 , GLY M:392 , SER M:393 , FAD M:601
BINDING SITE FOR RESIDUE OAA M 802
08
AC8
SOFTWARE
CYS N:148 , ILE N:149 , ASN N:150 , CYS N:151 , GLY N:152 , LEU N:153 , CYS N:154 , CYS N:214 , VAL N:218
BINDING SITE FOR RESIDUE SF4 N 244
09
AC9
SOFTWARE
CYS N:57 , ARG N:58 , ALA N:60 , ILE N:61 , CYS N:62 , GLY N:63 , SER N:64 , CYS N:65 , CYS N:77
BINDING SITE FOR RESIDUE FES N 245
10
BC1
SOFTWARE
CYS N:158 , GLN N:160 , CYS N:204 , THR N:205 , PHE N:206 , VAL N:207 , GLY N:208 , CYS N:210 , ALA N:221 , ILE N:224
BINDING SITE FOR RESIDUE F3S N 246
[
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
(5, 10)
Info
All PROSITE Patterns/Profiles
1: 2FE2S_FER_2 (B:15-96,N:15-96)
2: FRD_SDH_FAD_BINDING (A:42-51,M:42-51)
3: 2FE2S_FER_1 (B:57-65,N:57-65)
4: 4FE4S_FER_2 (B:139-168,N:139-168)
5: 4FE4S_FER_1 (B:148-159,N:148-159)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
2FE2S_FER_2
PS51085
2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
FRDB_ECOLI
16-97
2
B:15-96
N:15-96
2
FRD_SDH_FAD_BINDING
PS00504
Fumarate reductase / succinate dehydrogenase FAD-binding site.
FRDA_ECOLI
43-52
2
A:42-51
M:42-51
3
2FE2S_FER_1
PS00197
2Fe-2S ferredoxin-type iron-sulfur binding region signature.
FRDB_ECOLI
58-66
2
B:57-65
N:57-65
4
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
FRDB_ECOLI
140-169
2
B:139-168
N:139-168
5
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
FRDB_ECOLI
149-160
2
B:148-159
N:148-159
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_FAD_binding_2_3p4qM01 (M:6-396)
1b: PFAM_FAD_binding_2_3p4qM02 (M:6-396)
2a: PFAM_Succ_DH_flav_C_3p4qM03 (M:452-576)
2b: PFAM_Succ_DH_flav_C_3p4qM04 (M:452-576)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
FAD_binding_2
(21)
Escherichia coli O44:H18 (strain 042 / EAEC)
(4)
1a
FAD_binding_2-3p4qM01
M:6-396
1b
FAD_binding_2-3p4qM02
M:6-396
Clan
:
no clan defined [family: Succ_DH_flav_C]
(11)
Family
:
Succ_DH_flav_C
(11)
Escherichia coli O44:H18 (strain 042 / EAEC)
(4)
2a
Succ_DH_flav_C-3p4qM03
M:452-576
2b
Succ_DH_flav_C-3p4qM04
M:452-576
[
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
Chain C
Chain D
Chain M
Chain N
Chain O
Chain P
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 (722 KB)
Header - Asym.Unit
Biol.Unit 1 (350 KB)
Header - Biol.Unit 1
Biol.Unit 2 (364 KB)
Header - Biol.Unit 2
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
3P4Q
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
