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.
4BRB
Asym. Unit
Info
Asym.Unit (209 KB)
Biol.Unit 1 (104 KB)
Biol.Unit 2 (96 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 INTEGRAL MEMBRANE ENZYME DGKA-REF, DELTA 7
Authors
:
D. Li, M. Caffrey
Date
:
04 Jun 13 (Deposition) - 18 Jun 14 (Release) - 22 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.55
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Transferase, Lipid Metabolism, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Li, M. Caffrey
Renaturing Membrane Proteins In The Lipid Cubic Phase, A Nanoporous Membrane Mimetic.
Sci. Rep. V. 4 5806 2014
[
close entry info
]
Hetero Components
(4, 13)
Info
All Hetero Components
1a: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Na)
1b: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Nb)
1c: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Nc)
1d: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Nd)
1e: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Ne)
1f: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Nf)
1g: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Ng)
1h: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Nh)
1i: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Ni)
1j: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Nj)
2a: ACETATE ION (ACTa)
3a: CITRATE ANION (FLCa)
4a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
78N
10
Ligand/Ion
(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
2
ACT
1
Ligand/Ion
ACETATE ION
3
FLC
1
Ligand/Ion
CITRATE ANION
4
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:33 , 78N B:1122 , TRP C:117 , TRP D:25 , ALA D:29 , ARG D:32 , GLN D:33 , VAL D:36
BINDING SITE FOR RESIDUE 78N A1121
02
AC2
SOFTWARE
ARG A:22 , TRP A:25 , ILE A:26 , MET A:63 , 78N A:1123 , 78N A:1124
BINDING SITE FOR RESIDUE 78N A1122
03
AC3
SOFTWARE
TRP A:25 , LEU A:40 , 78N A:1122 , TRP C:47 , TRP C:112
BINDING SITE FOR RESIDUE 78N A1123
04
AC4
SOFTWARE
VAL A:42 , ALA A:46 , LEU A:48 , ARG A:55 , 78N A:1122 , 78N A:1125 , ILE B:110 , ILE B:114
BINDING SITE FOR RESIDUE 78N A1124
05
AC5
SOFTWARE
78N A:1124 , ILE B:110 , ILE B:114 , TRP B:117
BINDING SITE FOR RESIDUE 78N A1125
06
AC6
SOFTWARE
78N A:1121 , ALA B:46 , ARG B:55 , ILE C:110 , SER C:118 , GLN D:33 , LEU D:39 , VAL D:43
BINDING SITE FOR RESIDUE 78N B1122
07
AC7
SOFTWARE
GLN B:33 , GLU B:34 , GLU B:69 , ILE B:105 , ALA B:108 , TRP B:112
BINDING SITE FOR RESIDUE 78N B1123
08
AC8
SOFTWARE
GLU D:28 , GLU D:76 , FLC D:1123 , ACT D:1124
BINDING SITE FOR RESIDUE ZN D1122
09
AC9
SOFTWARE
GLU D:28 , GLU D:76 , ZN D:1122 , ACT D:1124
BINDING SITE FOR RESIDUE FLC D1123
10
BC1
SOFTWARE
GLU D:28 , GLU D:69 , ASN D:72 , GLU D:76 , ZN D:1122 , FLC D:1123
BINDING SITE FOR RESIDUE ACT D1124
11
BC2
SOFTWARE
ILE B:26 , ARG B:32 , GLY B:35 , VAL B:36 , LEU B:39 , MET B:63 , TRP D:47 , ASP D:49
BINDING SITE FOR RESIDUE 78N D1125
12
BC3
SOFTWARE
TRP B:47 , ASP B:49 , HOH B:2001 , ILE D:105 , VAL D:109 , ILE D:110
BINDING SITE FOR RESIDUE 78N D1126
13
BC4
SOFTWARE
ASP A:107 , VAL C:42 , ALA C:46 , ARG C:55 , MET C:63
BINDING SITE FOR RESIDUE 78N C1122
[
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, 6)
Info
All PROSITE Patterns/Profiles
1: DAGK_PROKAR (A:69-80,B:69-80,C:69-80,D:69-80,E:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DAGK_PROKAR
PS01069
Prokaryotic diacylglycerol kinase signature.
KDGL_ECOLI
70-81
6
A:69-80
B:69-80
C:69-80
D:69-80
E:69-80
F:69-80
[
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
(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
Chain C
Chain D
Chain E
Chain F
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 (209 KB)
Header - Asym.Unit
Biol.Unit 1 (104 KB)
Header - Biol.Unit 1
Biol.Unit 2 (96 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
4BRB
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
