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.
3HYK
Asym. Unit
Info
Asym.Unit (78 KB)
Biol.Unit 1 (68 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
2.31 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A HOLO-(ACYL-CARRIER-PROTEIN) SYNTHASE FROM BACILLUS ANTHRACIS STR. AMES IN COMPLEX WITH COA (3',5'-ADP)
Authors
:
A. S. Halavaty, G. Minasov, T. Skarina, O. Onopriyenko, L. Papazisi, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date
:
22 Jun 09 (Deposition) - 30 Jun 09 (Release) - 05 Dec 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.31
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Holo-(Acyl-Carrier-Protein) Synthase, Structural Genomics, Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Fatty Acid Biosynthesis, Lipid Synthesis, Magnesium, Metal-Binding, Transferase, Csgid
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. S. Halavaty, Y. Kim, G. Minasov, L. Shuvalova, I. Dubrovska, J. Winsor, M. Zhou, O. Onopriyenko, T. Skarina, L. Papazisi, K. Kwon, S. N. Peterson, A. Joachimiak, A. Savchenko, W. F. Anderson
Structural Characterization And Comparison Of Three Acyl-Carrier-Protein Synthases From Pathogenic Bacteria.
Acta Crystallogr. , Sect. D V. 68 1359 2012
[
close entry info
]
Hetero Components
(4, 30)
Info
All Hetero Components
1a: ADENOSINE-3'-5'-DIPHOSPHATE (A3Pa)
1b: ADENOSINE-3'-5'-DIPHOSPHATE (A3Pb)
1c: ADENOSINE-3'-5'-DIPHOSPHATE (A3Pc)
1d: ADENOSINE-3'-5'-DIPHOSPHATE (A3Pd)
1e: ADENOSINE-3'-5'-DIPHOSPHATE (A3Pe)
1f: ADENOSINE-3'-5'-DIPHOSPHATE (A3Pf)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
4a: SELENOMETHIONINE (MSEa)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
A3P
6
Ligand/Ion
ADENOSINE-3'-5'-DIPHOSPHATE
2
CL
6
Ligand/Ion
CHLORIDE ION
3
MG
9
Ligand/Ion
MAGNESIUM ION
4
MSE
9
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
A3P A:124 , HOH A:335 , A3P B:127 , HOH B:336 , HOH B:337 , HOH B:426
BINDING SITE FOR RESIDUE MG B 120
02
AC2
SOFTWARE
HIS A:103 , A3P A:124 , HOH A:331 , HOH A:332 , HOH B:328
BINDING SITE FOR RESIDUE MG A 120
03
AC3
SOFTWARE
A3P A:124 , HOH A:329 , ASP B:8 , GLU B:58 , HOH B:330 , HOH B:334
BINDING SITE FOR RESIDUE MG B 121
04
AC4
SOFTWARE
ILE B:68 , HOH B:212
BINDING SITE FOR RESIDUE CL B 122
05
AC5
SOFTWARE
ASP A:8 , GLU A:58 , HOH A:293 , HOH A:322 , SER C:102 , A3P C:126 , HOH C:303
BINDING SITE FOR RESIDUE MG A 121
06
AC6
SOFTWARE
ILE A:68 , HOH A:277
BINDING SITE FOR RESIDUE CL A 122
07
AC7
SOFTWARE
A3P A:125 , HOH A:296 , HOH A:301 , HOH A:321 , A3P C:126 , HOH C:302
BINDING SITE FOR RESIDUE MG A 123
08
AC8
SOFTWARE
SER B:102 , A3P B:126 , HOH B:312 , ASP C:8 , GLU C:58 , HOH C:290 , HOH C:313
BINDING SITE FOR RESIDUE MG C 120
09
AC9
SOFTWARE
HOH A:282 , HIS C:103 , A3P C:126 , HOH C:323 , HOH C:324
BINDING SITE FOR RESIDUE MG C 121
10
BC1
SOFTWARE
ILE C:68 , HOH C:319
BINDING SITE FOR RESIDUE CL C 122
11
BC2
SOFTWARE
HIS B:103 , A3P B:126 , HOH B:340 , HOH B:341 , HOH C:339
BINDING SITE FOR RESIDUE MG B 123
12
BC3
SOFTWARE
A3P B:126 , HOH B:310 , HOH B:381 , A3P C:125 , HOH C:311 , HOH C:318
BINDING SITE FOR RESIDUE MG C 123
13
BC4
SOFTWARE
GLU B:48 , PHE B:49 , GLY B:52 , ARG B:53 , A3P B:126
BINDING SITE FOR RESIDUE CL B 124
14
BC5
SOFTWARE
ILE C:10 , GLU C:11 , ARG C:14 , HOH C:397 , HOH C:398
BINDING SITE FOR RESIDUE CL C 124
15
BC6
SOFTWARE
SER A:104 , GLU B:11 , ARG B:14 , HOH B:147 , HOH B:333
BINDING SITE FOR RESIDUE CL B 125
16
BC7
SOFTWARE
ARG B:45 , ARG B:53 , ASN B:81 , ARG B:84 , GLY B:85 , LYS B:86 , PRO B:87 , ILE B:101 , SER B:102 , HIS B:103 , MG B:123 , CL B:124 , HOH B:162 , HOH B:228 , HOH B:286 , HOH B:309 , HOH B:310 , HOH B:312 , HOH B:341 , HOH B:381 , ASP C:8 , GLU C:58 , LYS C:62 , GLY C:65 , THR C:66 , GLY C:67 , MG C:120 , MG C:123 , A3P C:125 , HOH C:311 , HOH C:313 , HOH C:339
BINDING SITE FOR RESIDUE A3P B 126
17
BC8
SOFTWARE
LYS B:70 , GLU B:71 , A3P B:126 , HOH B:310 , HOH B:312 , ARG C:14 , MSE C:18 , ARG C:28 , MG C:123 , HOH C:287 , HOH C:288 , HOH C:291 , HOH C:292 , HOH C:304 , HOH C:311 , HOH C:315 , HOH C:316 , HOH C:317 , HOH C:318 , HOH C:339 , HOH C:399
BINDING SITE FOR RESIDUE A3P C 125
18
BC9
SOFTWARE
A3P A:124 , HOH A:329 , ARG B:14 , MSE B:18 , ARG B:28 , ARG B:84 , MG B:120 , HOH B:141 , HOH B:264 , HOH B:328 , HOH B:336 , HOH B:337 , HOH B:342 , HOH B:377 , HOH B:426 , LYS C:70 , GLU C:71 , HOH C:149
BINDING SITE FOR RESIDUE A3P B 127
19
CC1
SOFTWARE
ARG A:45 , ARG A:53 , ASN A:81 , ARG A:84 , GLY A:85 , LYS A:86 , PRO A:87 , ILE A:101 , SER A:102 , HIS A:103 , MG A:120 , HOH A:129 , HOH A:136 , HOH A:138 , HOH A:269 , HOH A:329 , HOH A:331 , HOH A:335 , HOH A:343 , HOH A:424 , ASP B:8 , GLU B:58 , LYS B:62 , GLY B:65 , THR B:66 , GLY B:67 , MG B:120 , MG B:121 , A3P B:127 , HOH B:328 , HOH B:334 , HOH B:336 , HOH B:337
BINDING SITE FOR RESIDUE A3P A 124
20
CC2
SOFTWARE
ASP A:8 , GLU A:58 , LYS A:62 , GLY A:65 , THR A:66 , GLY A:67 , MG A:121 , MG A:123 , A3P A:125 , HOH A:282 , HOH A:296 , HOH A:301 , HOH A:322 , ARG C:45 , ARG C:53 , ASN C:81 , ARG C:84 , GLY C:85 , LYS C:86 , PRO C:87 , ILE C:101 , SER C:102 , HIS C:103 , MG C:121 , HOH C:131 , HOH C:135 , HOH C:302 , HOH C:303 , HOH C:324 , HOH C:325 , HOH C:326 , HOH C:422
BINDING SITE FOR RESIDUE A3P C 126
21
CC3
SOFTWARE
ARG A:14 , ARG A:28 , LYS A:70 , GLU A:71 , MG A:123 , HOH A:194 , HOH A:279 , HOH A:282 , HOH A:283 , HOH A:294 , HOH A:295 , HOH A:296 , HOH A:297 , HOH A:298 , HOH A:301 , HOH A:321 , HOH A:383 , HOH A:388 , HOH A:404 , ARG C:84 , A3P C:126 , HOH C:303
BINDING SITE FOR RESIDUE A3P A 125
[
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
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3hyka_ (A:)
1b: SCOP_d3hykb_ (B:)
1c: SCOP_d3hykc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
4'-phosphopantetheinyl transferase
(26)
Superfamily
:
4'-phosphopantetheinyl transferase
(26)
Family
:
automated matches
(19)
Protein domain
:
automated matches
(19)
Anthrax bacillus (Bacillus anthracis) [TaxId: 1392]
(1)
1a
d3hyka_
A:
1b
d3hykb_
B:
1c
d3hykc_
C:
[
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 (78 KB)
Header - Asym.Unit
Biol.Unit 1 (68 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
3HYK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
