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.
2GMH
Asym. Unit
Info
Asym.Unit (207 KB)
Biol.Unit 1 (105 KB)
Biol.Unit 2 (99 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF PORCINE ELECTRON TRANSFER FLAVOPROTEIN-UBIQUINONE OXIDOREDUCTASE IN COMPLEXED WITH UBIQUINONE
Authors
:
J. Zhang, F. E. Frerman, J. -J. P. Kim
Date
:
06 Apr 06 (Deposition) - 17 Oct 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Electron-Transfer, Oxidoreductase, Flavoprotein, Ubiquinone
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Zhang, F. E. Frerman, J. J. Kim
Structure Of Electron Transfer Flavoprotein-Ubiquinone Oxidoreductase And Electron Transfer To The Mitochondrial Ubiquinone Pool.
Proc. Natl. Acad. Sci. Usa V. 103 16212 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(6, 20)
Info
All Hetero Components
1a: 2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHY... (BHGa)
1b: 2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHY... (BHGb)
1c: 2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHY... (BHGc)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
3a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
3b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
4a: SODIUM ION (NAa)
5a: IRON/SULFUR CLUSTER (SF4a)
5b: IRON/SULFUR CLUSTER (SF4b)
6a: 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,... (UQ5a)
6b: 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,... (UQ5b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BHG
3
Ligand/Ion
2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL
2
EDO
10
Ligand/Ion
1,2-ETHANEDIOL
3
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
4
NA
1
Ligand/Ion
SODIUM ION
5
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
6
UQ5
2
Ligand/Ion
2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE
[
close Hetero Component info
]
Sites
(20, 20)
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)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:424 , PHE A:441 , PHE A:445 , MET A:448 , PRO A:450 , TRP A:451
BINDING SITE FOR RESIDUE BHG A 616
02
AC2
SOFTWARE
LEU A:128 , PRO A:129 , GLY A:130 , HIS A:269 , ILE A:428 , TRP A:443
BINDING SITE FOR RESIDUE BHG A 617
03
AC3
SOFTWARE
PHE B:441
BINDING SITE FOR RESIDUE BHG B 618
04
AC4
SOFTWARE
ASN A:232 , HOH A:828 , HOH A:874 , HOH A:935 , HOH A:944 , HOH A:966
BINDING SITE FOR RESIDUE NA A 1070
05
AC5
SOFTWARE
LEU A:504 , CYS A:528 , CYS A:553 , VAL A:554 , CYS A:556 , LYS A:557 , CYS A:559 , TRP A:570
BINDING SITE FOR RESIDUE SF4 A 610
06
AC6
SOFTWARE
VAL A:41 , GLY A:42 , GLY A:44 , PRO A:45 , ALA A:46 , GLU A:71 , LYS A:72 , HIS A:79 , SER A:82 , GLY A:83 , ALA A:84 , CYS A:85 , ALA A:166 , ALA A:167 , ALA A:212 , GLU A:213 , GLY A:214 , HIS A:218 , LEU A:219 , ARG A:331 , GLY A:353 , CYS A:354 , ILE A:364 , LYS A:365 , GLY A:366 , THR A:367 , HOH A:741 , HOH A:769 , HOH A:792 , HOH A:840 , HOH A:926 , HOH A:931 , HOH A:936 , HOH A:942 , HOH A:994 , HOH A:1043
BINDING SITE FOR RESIDUE FAD A 611
07
AC7
SOFTWARE
PHE A:114 , MET A:133 , HIS A:260 , VAL A:262 , TYR A:271 , GLY A:272 , GLY A:273 , SER A:274 , ILE A:364 , GLY A:434 , MET A:435 , THR A:438 , GLY A:439
BINDING SITE FOR RESIDUE UQ5 A 612
08
AC8
SOFTWARE
LEU B:504 , CYS B:528 , PRO B:529 , ALA B:530 , VAL B:532 , TYR B:533 , CYS B:553 , VAL B:554 , CYS B:556 , LYS B:557 , CYS B:559 , TRP B:570
BINDING SITE FOR RESIDUE SF4 B 613
09
AC9
SOFTWARE
VAL B:41 , GLY B:42 , PRO B:45 , ALA B:46 , GLU B:71 , LYS B:72 , HIS B:79 , SER B:82 , GLY B:83 , ALA B:84 , CYS B:85 , ALA B:167 , GLU B:213 , GLY B:214 , HIS B:218 , PHE B:275 , TYR B:277 , ARG B:331 , GLY B:353 , CYS B:354 , ILE B:364 , LYS B:365 , GLY B:366 , THR B:367 , VAL B:572 , HOH B:859 , HOH B:1013
BINDING SITE FOR RESIDUE FAD B 614
10
BC1
SOFTWARE
PHE B:114 , MET B:133 , HIS B:260 , THR B:261 , VAL B:262 , GLY B:272 , GLY B:273 , SER B:274 , ILE B:364 , GLY B:434 , MET B:435 , THR B:438 , GLY B:439
BINDING SITE FOR RESIDUE UQ5 B 615
11
BC2
SOFTWARE
GLN A:480 , GLU A:497 , GLU A:574 , GLY A:577 , HOH A:811
BINDING SITE FOR RESIDUE EDO A 619
12
BC3
SOFTWARE
PRO B:129 , GLY B:130 , ARG B:268 , TRP B:443
BINDING SITE FOR RESIDUE EDO B 620
13
BC4
SOFTWARE
VAL A:489 , ALA A:490 , THR A:494 , HOH A:857
BINDING SITE FOR RESIDUE EDO A 621
14
BC5
SOFTWARE
HIS A:12 , TYR A:13 , ALA A:168 , HIS A:218 , VAL A:571 , VAL A:572
BINDING SITE FOR RESIDUE EDO A 622
15
BC6
SOFTWARE
ILE A:9 , THR A:10 , THR A:11 , HIS A:12 , ALA A:502 , LEU A:504 , THR A:505 , ILE A:548
BINDING SITE FOR RESIDUE EDO A 623
16
BC7
SOFTWARE
LYS A:324 , ARG A:325 , PHE A:483 , GLY A:493 , ASN A:495 , ALA A:580 , HOH A:767 , HOH A:905 , HOH A:919 , HOH A:993
BINDING SITE FOR RESIDUE EDO A 624
17
BC8
SOFTWARE
ARG A:268
BINDING SITE FOR RESIDUE EDO A 625
18
BC9
SOFTWARE
GLN A:525 , HOH A:934
BINDING SITE FOR RESIDUE EDO A 626
19
CC1
SOFTWARE
ASN A:280 , GLY A:282 , HOH A:1050
BINDING SITE FOR RESIDUE EDO A 627
20
CC2
SOFTWARE
PHE A:32 , ALA A:33
BINDING SITE FOR RESIDUE EDO A 628
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_FER_2 (A:544-573,B:544-573)
;
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.
ETFD_PIG
577-606
2
A:544-573
B:544-573
[
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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2gmha2 (A:237-335)
1b: SCOP_d2gmhb2 (B:237-335)
2a: SCOP_d2gmha3 (A:483-584)
2b: SCOP_d2gmhb3 (B:483-584)
3a: SCOP_d2gmha1 (A:4-236,A:336-482)
3b: SCOP_d2gmhb1 (B:7-236,B:336-482)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FAD-linked reductases, C-terminal domain
(181)
Superfamily
:
FAD-linked reductases, C-terminal domain
(181)
Family
:
Electron transfer flavoprotein-ubiquinone oxidoreductase-like
(2)
Protein domain
:
Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO
(2)
Pig (Sus scrofa) [TaxId: 9823]
(2)
1a
d2gmha2
A:237-335
1b
d2gmhb2
B:237-335
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
4Fe-4S ferredoxins
(143)
Family
:
ETF-QO domain-like
(2)
Protein domain
:
Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO
(2)
Pig (Sus scrofa) [TaxId: 9823]
(2)
2a
d2gmha3
A:483-584
2b
d2gmhb3
B:483-584
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FAD/NAD(P)-binding domain
(331)
Superfamily
:
FAD/NAD(P)-binding domain
(331)
Family
:
FAD-linked reductases, N-terminal domain
(156)
Protein domain
:
Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO
(2)
Pig (Sus scrofa) [TaxId: 9823]
(2)
3a
d2gmha1
A:4-236,A:336-482
3b
d2gmhb1
B:7-236,B:336-482
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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 (207 KB)
Header - Asym.Unit
Biol.Unit 1 (105 KB)
Header - Biol.Unit 1
Biol.Unit 2 (99 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
2GMH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
