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.
4O6M
Asym. Unit
Info
Asym.Unit (223 KB)
Biol.Unit 1 (215 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 AF2299, A CDP-ALCOHOL PHOSPHOTRANSFERASE (CMP-BOUND)
Authors
:
O. B. Clarke, G. Sciara, D. Tomasek, S. Banerjee, K. R. Rajashankar, L. S F. Mancia, New York Consortium On Membrane Protein Structure
Date
:
22 Dec 13 (Deposition) - 14 May 14 (Release) - 13 Aug 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Cdp-Alcohol Phosphotransferase, Membrane Protein, Structural Genomics, Psi-Biology, New York Consortium On Membrane Protein Structure, Nycomps, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Sciara, O. B. Clarke, D. Tomasek, B. Kloss, S. Tabuso, R. Byfield, R. Cohn, S. Banerjee, K. R. Rajashankar, V. Slavkovic, J. H. Graziano, L. Shapiro, F. Mancia
Structural Basis For Catalysis In A Cdp-Alcohol Phosphotransferase.
Nat Commun V. 5 4068 2014
[
close entry info
]
Hetero Components
(4, 35)
Info
All Hetero Components
1a: CYTIDINE-5'-MONOPHOSPHATE (C5Pa)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: 1-MONOOLEOYL-RAC-GLYCEROL (MPGa)
3b: 1-MONOOLEOYL-RAC-GLYCEROL (MPGb)
3c: 1-MONOOLEOYL-RAC-GLYCEROL (MPGc)
3d: 1-MONOOLEOYL-RAC-GLYCEROL (MPGd)
3e: 1-MONOOLEOYL-RAC-GLYCEROL (MPGe)
3f: 1-MONOOLEOYL-RAC-GLYCEROL (MPGf)
3g: 1-MONOOLEOYL-RAC-GLYCEROL (MPGg)
3h: 1-MONOOLEOYL-RAC-GLYCEROL (MPGh)
3i: 1-MONOOLEOYL-RAC-GLYCEROL (MPGi)
3j: 1-MONOOLEOYL-RAC-GLYCEROL (MPGj)
3k: 1-MONOOLEOYL-RAC-GLYCEROL (MPGk)
3l: 1-MONOOLEOYL-RAC-GLYCEROL (MPGl)
3m: 1-MONOOLEOYL-RAC-GLYCEROL (MPGm)
3n: 1-MONOOLEOYL-RAC-GLYCEROL (MPGn)
3o: 1-MONOOLEOYL-RAC-GLYCEROL (MPGo)
3p: 1-MONOOLEOYL-RAC-GLYCEROL (MPGp)
3q: 1-MONOOLEOYL-RAC-GLYCEROL (MPGq)
3r: 1-MONOOLEOYL-RAC-GLYCEROL (MPGr)
3s: 1-MONOOLEOYL-RAC-GLYCEROL (MPGs)
3t: 1-MONOOLEOYL-RAC-GLYCEROL (MPGt)
3u: 1-MONOOLEOYL-RAC-GLYCEROL (MPGu)
3v: 1-MONOOLEOYL-RAC-GLYCEROL (MPGv)
3w: 1-MONOOLEOYL-RAC-GLYCEROL (MPGw)
3x: 1-MONOOLEOYL-RAC-GLYCEROL (MPGx)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
C5P
1
Ligand/Ion
CYTIDINE-5'-MONOPHOSPHATE
2
CA
2
Ligand/Ion
CALCIUM ION
3
MPG
24
Ligand/Ion
1-MONOOLEOYL-RAC-GLYCEROL
4
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(29, 29)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:148 , ASP A:214 , ASP A:217 , ASP A:235 , ASP A:239 , HOH A:574 , HOH A:576 , HOH A:580
BINDING SITE FOR RESIDUE CA A 401
02
AC2
SOFTWARE
VAL A:179 , MPG A:404 , MPG A:405
BINDING SITE FOR RESIDUE MPG A 402
03
AC3
SOFTWARE
MPG A:402
BINDING SITE FOR RESIDUE MPG A 404
04
AC4
SOFTWARE
MPG A:402
BINDING SITE FOR RESIDUE MPG A 405
05
AC5
SOFTWARE
LEU A:326 , PHE A:330
BINDING SITE FOR RESIDUE MPG A 407
06
AC6
SOFTWARE
LEU A:193
BINDING SITE FOR RESIDUE MPG A 408
07
AC7
SOFTWARE
THR A:173 , ASN A:175 , HOH A:553
BINDING SITE FOR RESIDUE SO4 A 410
08
AC8
SOFTWARE
ARG A:240 , ILE A:275 , ALA A:276 , THR A:300 , ARG A:301 , ARG A:304 , HOH A:540 , HOH A:542
BINDING SITE FOR RESIDUE SO4 A 411
09
AC9
SOFTWARE
GLY A:68 , ARG A:69
BINDING SITE FOR RESIDUE SO4 A 412
10
BC1
SOFTWARE
PRO A:292 , GLU A:293 , ARG A:334 , ALA A:338 , HOH A:564
BINDING SITE FOR RESIDUE SO4 A 413
11
BC2
SOFTWARE
ASP B:214 , ASP B:217 , ASP B:235 , C5P B:422 , HOH B:578
BINDING SITE FOR RESIDUE CA B 401
12
BC3
SOFTWARE
THR B:170
BINDING SITE FOR RESIDUE MPG B 404
13
BC4
SOFTWARE
LEU B:326
BINDING SITE FOR RESIDUE MPG B 405
14
BC5
SOFTWARE
VAL B:322
BINDING SITE FOR RESIDUE MPG B 406
15
BC6
SOFTWARE
TYR B:230 , MPG B:413
BINDING SITE FOR RESIDUE MPG B 407
16
BC7
SOFTWARE
ALA B:310
BINDING SITE FOR RESIDUE MPG B 408
17
BC8
SOFTWARE
PHE A:303 , MPG B:416
BINDING SITE FOR RESIDUE MPG B 409
18
BC9
SOFTWARE
MPG B:417
BINDING SITE FOR RESIDUE MPG B 410
19
CC1
SOFTWARE
MPG B:413
BINDING SITE FOR RESIDUE MPG B 411
20
CC2
SOFTWARE
LEU B:186 , MPG B:407 , MPG B:411
BINDING SITE FOR RESIDUE MPG B 413
21
CC3
SOFTWARE
MPG B:415
BINDING SITE FOR RESIDUE MPG B 414
22
CC4
SOFTWARE
LEU B:193 , TYR B:252 , MPG B:414
BINDING SITE FOR RESIDUE MPG B 415
23
CC5
SOFTWARE
VAL A:322 , MPG B:409
BINDING SITE FOR RESIDUE MPG B 416
24
CC6
SOFTWARE
PHE A:295 , MPG B:410 , HOH B:532 , HOH B:579
BINDING SITE FOR RESIDUE MPG B 417
25
CC7
SOFTWARE
GLY B:68 , ARG B:69
BINDING SITE FOR RESIDUE SO4 B 418
26
CC8
SOFTWARE
TYR B:146 , ARG B:240 , ILE B:275 , ALA B:276 , THR B:300 , ARG B:301 , ARG B:304 , HOH B:534 , HOH B:569 , HOH B:576
BINDING SITE FOR RESIDUE SO4 B 419
27
CC9
SOFTWARE
GLN B:176 , HOH B:539 , HOH B:557 , HOH B:564
BINDING SITE FOR RESIDUE SO4 B 420
28
DC1
SOFTWARE
TYR B:197
BINDING SITE FOR RESIDUE SO4 B 421
29
DC2
SOFTWARE
LYS B:136 , ARG B:157 , PRO B:174 , ASN B:175 , THR B:178 , ASP B:214 , GLY B:215 , ASP B:217 , GLY B:218 , ARG B:222 , GLU B:227 , SER B:228 , GLY B:231 , ALA B:232 , ASP B:235 , CA B:401 , HOH B:518 , HOH B:526 , HOH B:531 , HOH B:578
BINDING SITE FOR RESIDUE C5P B 422
[
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
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 (223 KB)
Header - Asym.Unit
Biol.Unit 1 (215 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
4O6M
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
