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.
2R46
Asym. Unit
Info
Asym.Unit (183 KB)
Biol.Unit 1 (91 KB)
Biol.Unit 2 (89 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 ESCHERICHIA COLI GLYCEROL-3-PHOSPHATE DEHYDROGENASE IN COMPLEX WITH 2-PHOSPHOPYRUVIC ACID.
Authors
:
J. I. Yeh, S. Du, U. Chinte
Date
:
30 Aug 07 (Deposition) - 29 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Glpd, Cytoplasm, Fad, Flavoprotein, Glycerol Metabolism, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. I. Yeh, U. Chinte, S. Du
Structure Of Glycerol-3-Phosphate Dehydrogenase, An Essential Monotopic Membrane Enzyme Involved In Respiration And Metabolism
Proc. Natl. Acad. Sci. Usa V. 105 3280 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(6, 34)
Info
All Hetero Components
1a: B-OCTYLGLUCOSIDE (BOGa)
1b: B-OCTYLGLUCOSIDE (BOGb)
1c: B-OCTYLGLUCOSIDE (BOGc)
1d: B-OCTYLGLUCOSIDE (BOGd)
1e: B-OCTYLGLUCOSIDE (BOGe)
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)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
3a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
3b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
4a: IMIDAZOLE (IMDa)
5a: PHOSPHOENOLPYRUVATE (PEPa)
5b: PHOSPHOENOLPYRUVATE (PEPb)
6a: N-(TRIS(HYDROXYMETHYL)METHYL)-3-AM... (T3Aa)
6b: N-(TRIS(HYDROXYMETHYL)METHYL)-3-AM... (T3Ab)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BOG
5
Ligand/Ion
B-OCTYLGLUCOSIDE
2
EDO
22
Ligand/Ion
1,2-ETHANEDIOL
3
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
4
IMD
1
Ligand/Ion
IMIDAZOLE
5
PEP
2
Ligand/Ion
PHOSPHOENOLPYRUVATE
6
T3A
2
Ligand/Ion
N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONICACID
[
close Hetero Component info
]
Sites
(32, 32)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:53 , ARG A:54 , GLU A:57 , LEU A:89 , ARG A:96 , ILE A:101 , GLY A:104
BINDING SITE FOR RESIDUE BOG A 900
02
AC2
SOFTWARE
LEU B:53 , ARG B:54 , GLU B:57 , ARG B:96 , ILE B:101 , GLY B:104 , LEU B:105
BINDING SITE FOR RESIDUE BOG B 900
03
AC3
SOFTWARE
ALA A:98 , TRP A:99 , ARG A:102 , ARG A:137
BINDING SITE FOR RESIDUE BOG A 800
04
AC4
SOFTWARE
ALA B:98 , TRP B:99 , ARG B:102 , ARG B:137
BINDING SITE FOR RESIDUE BOG B 800
05
AC5
SOFTWARE
HIS A:91 , PRO A:93 , ALA A:98 , ARG A:137 , ASP B:322
BINDING SITE FOR RESIDUE BOG A 1949
06
AC6
SOFTWARE
THR B:271 , ASP B:272
BINDING SITE FOR RESIDUE EDO B 901
07
AC7
SOFTWARE
ALA B:34 , TRP B:209
BINDING SITE FOR RESIDUE EDO B 902
08
AC8
SOFTWARE
TRP B:311 , TRP B:468
BINDING SITE FOR RESIDUE EDO B 903
09
AC9
SOFTWARE
SER B:43 , TRP B:468 , ARG B:469
BINDING SITE FOR RESIDUE EDO B 904
10
BC1
SOFTWARE
ALA A:34 , LYS A:280
BINDING SITE FOR RESIDUE EDO A 1950
11
BC2
SOFTWARE
SER A:43 , TRP A:468 , ARG A:469
BINDING SITE FOR RESIDUE EDO A 1951
12
BC3
SOFTWARE
ILE B:309
BINDING SITE FOR RESIDUE EDO B 905
13
BC4
SOFTWARE
GLN A:157 , ARG A:161 , PRO A:387 , ARG B:405
BINDING SITE FOR RESIDUE EDO A 1953
14
BC5
SOFTWARE
ARG A:254 , THR A:271 , ASP A:272
BINDING SITE FOR RESIDUE EDO A 1954
15
BC6
SOFTWARE
LEU A:438 , GLU A:448
BINDING SITE FOR RESIDUE EDO A 1955
16
BC7
SOFTWARE
ARG A:405 , GLN B:157 , ARG B:161 , PRO B:387
BINDING SITE FOR RESIDUE EDO A 1956
17
BC8
SOFTWARE
ARG B:88 , PHE B:125 , SER B:129 , GLN B:242 , TYR B:246
BINDING SITE FOR RESIDUE EDO B 907
18
BC9
SOFTWARE
PRO B:208 , GLN B:212 , LEU B:228 , PRO B:279
BINDING SITE FOR RESIDUE EDO B 908
19
CC1
SOFTWARE
ALA A:400 , ARG A:404
BINDING SITE FOR RESIDUE EDO A 1957
20
CC2
SOFTWARE
GLN A:157 , ASP A:456 , HIS A:457 , GLU A:458 , TRP A:459 , ARG B:405
BINDING SITE FOR RESIDUE T3A A 7066
21
CC3
SOFTWARE
ARG A:405 , GLN B:157 , ASP B:456 , HIS B:457 , GLU B:458 , TRP B:459
BINDING SITE FOR RESIDUE T3A B 7066
22
CC4
SOFTWARE
GLU A:165
BINDING SITE FOR RESIDUE EDO A 7067
23
CC5
SOFTWARE
GLU B:165 , TRP B:459
BINDING SITE FOR RESIDUE EDO B 7067
24
CC6
SOFTWARE
SER A:174 , ASP A:216 , GLY A:217 , HIS A:219
BINDING SITE FOR RESIDUE EDO A 7068
25
CC7
SOFTWARE
TRP A:311 , THR A:312
BINDING SITE FOR RESIDUE EDO A 7069
26
CC8
SOFTWARE
ALA B:463 , ASP B:464
BINDING SITE FOR RESIDUE IMD B 7068
27
CC9
SOFTWARE
ILE A:9 , GLY A:10 , GLY A:12 , ILE A:13 , ASN A:14 , LEU A:32 , GLU A:33 , ALA A:34 , CYS A:39 , ALA A:40 , THR A:41 , SER A:42 , ALA A:44 , SER A:45 , SER A:46 , LYS A:47 , LEU A:48 , ALA A:172 , THR A:206 , GLY A:207 , PRO A:208 , GLY A:231 , THR A:270 , ARG A:317 , GLY A:353 , LYS A:354 , LEU A:355 , THR A:356
BINDING SITE FOR RESIDUE FAD A 600
28
DC1
SOFTWARE
ILE B:9 , GLY B:10 , GLY B:12 , ILE B:13 , ASN B:14 , LEU B:32 , GLU B:33 , ALA B:34 , CYS B:39 , ALA B:40 , THR B:41 , SER B:42 , ALA B:44 , SER B:45 , SER B:46 , LYS B:47 , LEU B:48 , HIS B:50 , ALA B:172 , THR B:206 , PRO B:208 , GLY B:231 , THR B:270 , ARG B:317 , GLY B:353 , LYS B:354 , LEU B:355 , THR B:356
BINDING SITE FOR RESIDUE FAD B 600
29
DC2
SOFTWARE
ARG A:54 , TYR A:55 , ARG A:254 , ILE A:255 , PHE A:257 , THR A:270 , ASP A:272 , ARG A:317 , ARG A:332
BINDING SITE FOR RESIDUE PEP A 700
30
DC3
SOFTWARE
ARG B:54 , TYR B:55 , ARG B:254 , ILE B:255 , PHE B:257 , THR B:270 , ASP B:272 , ARG B:317 , ARG B:332 , LYS B:354
BINDING SITE FOR RESIDUE PEP B 700
31
DC4
SOFTWARE
PRO A:208 , TRP A:209 , GLN A:212 , LEU A:228 , PRO A:279
BINDING SITE FOR RESIDUE EDO A 7070
32
DC5
SOFTWARE
TRP B:468 , GLY B:474 , MET B:475
BINDING SITE FOR RESIDUE EDO B 7069
[
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, 4)
Info
All PROSITE Patterns/Profiles
1: FAD_G3PDH_1 (A:9-26,B:9-26)
2: FAD_G3PDH_2 (A:352-362,B:352-362)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FAD_G3PDH_1
PS00977
FAD-dependent glycerol-3-phosphate dehydrogenase signature 1.
GLPD_ECOLI
9-26
2
A:9-26
B:9-26
2
FAD_G3PDH_2
PS00978
FAD-dependent glycerol-3-phosphate dehydrogenase signature 2.
GLPD_ECOLI
352-362
2
A:352-362
B:352-362
[
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
(1, 2)
Info
all PFAM domains
1a: PFAM_DAO_2r46B01 (B:5-359)
1b: PFAM_DAO_2r46B02 (B:5-359)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
DAO
(25)
Escherichia coli (strain K12)
(6)
1a
DAO-2r46B01
B:5-359
1b
DAO-2r46B02
B:5-359
[
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 (183 KB)
Header - Asym.Unit
Biol.Unit 1 (91 KB)
Header - Biol.Unit 1
Biol.Unit 2 (89 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
2R46
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
