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.
4UXX
Asym. Unit
Info
Asym.Unit (127 KB)
Biol.Unit 1 (118 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 DELTA4-DGKA WITH AMPPCP IN 9.9 MAG
Authors
:
D. Li, L. Vogeley, M. Caffrey
Date
:
27 Aug 14 (Deposition) - 30 Sep 15 (Release) - 13 Jan 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Transferase, Atp Analogue, Dgka, Diacylglyerol Kinase, In Meso Crystallization, Lipid Cubic Phase, Lipidic Cubic Phase, Lipid Mesophase, Lipidic Mesophase, Membrane Protein, 9. 9 Mag, Monoacylglycerol, Non- Hydrolyzable Atp Analogue, Nucleotide Analogue
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Li, P. J. Stansfeld, M. S. P. Sansom, A. Keogh, L. Vogeley, N. Howe, J. A. Lyons, D. Aragao, P. Fromme, R. Fromme, S. Basu, I. Grotjohann, C. Kupitz, K. Rendek, U. Weierstall, N. A. Zatsepin, V. Cherezov, W. Liu, S. Bandaru, N. J. English, C. Gati, A. Barty, O. Yefanov, H. N. Chapman, K. Diederichs, M. Messerschmidt, S. Boutet, G. J. Williams, M. Marvin Seibert, M. Caffrey
Ternary Structure Reveals Mechanism Of A Membrane Diacylglycerol Kinase.
Nat. Commun. V. 6 10140 2015
[
close entry info
]
Hetero Components
(7, 17)
Info
All Hetero Components
1a: PHOSPHOMETHYLPHOSPHONIC ACID ADENY... (ACPa)
2a: ACETATE ION (ACTa)
2b: ACETATE ION (ACTb)
2c: ACETATE ION (ACTc)
3a: CHLORIDE ION (CLa)
4a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
6a: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCa)
6b: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCb)
6c: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCc)
6d: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCd)
6e: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCe)
6f: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCf)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACP
1
Ligand/Ion
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2
ACT
3
Ligand/Ion
ACETATE ION
3
CL
1
Ligand/Ion
CHLORIDE ION
4
MPD
1
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
5
NA
3
Ligand/Ion
SODIUM ION
6
OLC
6
Ligand/Ion
(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
7
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU C:28 , GLU C:76 , ACP C:1123
BINDING SITE FOR RESIDUE ZN C1121
02
AC2
SOFTWARE
GLU C:76 , ACP C:1123
BINDING SITE FOR RESIDUE ZN C1122
03
AC3
SOFTWARE
ASN A:27 , ALA A:29 , ARG A:32
BINDING SITE FOR RESIDUE CL A1121
04
AC4
SOFTWARE
ARG B:9 , TYR B:16 , HOH B:2001 , GLU C:28 , ASN C:72 , GLU C:76 , GLU C:85 , TYR C:86 , HIS C:87 , SER C:90 , GLY C:91 , LYS C:94 , ASP C:95 , ZN C:1121 , ZN C:1122 , OLC C:1125 , HOH C:2004
BINDING SITE FOR RESIDUE ACP C1123
05
AC5
SOFTWARE
ARG A:81 , GLU B:88 , LEU B:89 , SER B:90 , ARG B:92
BINDING SITE FOR RESIDUE MPD B1122
06
AC6
SOFTWARE
GLU A:28 , GLU A:76 , ACT A:1123
BINDING SITE FOR RESIDUE NA A1122
07
AC7
SOFTWARE
GLU A:28 , GLU A:76 , NA A:1122
BINDING SITE FOR RESIDUE ACT A1123
08
AC8
SOFTWARE
ARG B:9 , ILE B:10 , ALA C:30 , GLN C:33 , GLU C:34 , CYS C:113 , OLC C:1125
BINDING SITE FOR RESIDUE OLC C1124
09
AC9
SOFTWARE
SER A:17 , CYS A:113 , TRP A:117 , GLU B:34 , ALA B:37 , ILE B:44 , GLU B:69 , ASN B:72 , LEU B:102 , OLC B:1124
BINDING SITE FOR RESIDUE OLC B1123
10
BC1
SOFTWARE
ILE A:10 , TRP A:117 , GLN B:33 , GLU B:34 , TRP B:112 , TRP B:117 , OLC B:1123
BINDING SITE FOR RESIDUE OLC B1124
11
BC2
SOFTWARE
TRP A:18 , TRP A:25 , ILE A:26
BINDING SITE FOR RESIDUE OLC A1124
12
BC3
SOFTWARE
GLN A:33 , GLU A:34 , ALA A:37 , ILE A:44 , VAL A:62 , ALA A:108 , VAL A:109 , TRP A:112 , LEU A:116 , LEU B:39 , LEU B:40 , TRP B:47
BINDING SITE FOR RESIDUE OLC A1125
13
BC4
SOFTWARE
ALA B:13 , SER B:17 , GLU C:69 , ASN C:72 , SER C:98 , LEU C:102 , ILE C:106 , VAL C:109 , ACP C:1123 , OLC C:1124
BINDING SITE FOR RESIDUE OLC C1125
14
BC5
SOFTWARE
GLU B:76 , GLY B:83 , SER B:84 , GLU B:85 , TYR B:86 , HIS B:87 , LYS B:94 , NA B:1126
BINDING SITE FOR RESIDUE ACT B1125
15
BC6
SOFTWARE
GLU B:28 , GLU B:76 , ACT B:1125
BINDING SITE FOR RESIDUE NA B1126
16
BC7
SOFTWARE
GLU C:88
BINDING SITE FOR RESIDUE NA C1126
17
BC8
SOFTWARE
HIS A:119
BINDING SITE FOR RESIDUE ACT A1126
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
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 (127 KB)
Header - Asym.Unit
Biol.Unit 1 (118 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
4UXX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help