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.
2Y27
Asym. Unit
Info
Asym.Unit (168 KB)
Biol.Unit 1 (159 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 PAAK1 IN COMPLEX WITH ATP FROM BURKHOLDERIA CENOCEPACIA
Authors
:
A. Law, M. J. Boulanger
Date
:
13 Dec 10 (Deposition) - 04 May 11 (Release) - 12 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Ligase, Phenylacetic Acid Degradation Pathway
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Law, M. J. Boulanger
Defining A Structural And Kinetic Rationale For Paralogous Copies Of Phenylacetate-Coa Ligases From The Cystic Fibrosi Pathogen Burkholderia Cenocepacia J2315.
J. Biol. Chem. V. 286 15577 2011
[
close entry info
]
Hetero Components
(7, 48)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: BETA-MERCAPTOETHANOL (BMEa)
2b: BETA-MERCAPTOETHANOL (BMEb)
2c: BETA-MERCAPTOETHANOL (BMEc)
2d: BETA-MERCAPTOETHANOL (BMEd)
2e: BETA-MERCAPTOETHANOL (BMEe)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
5a: SELENOMETHIONINE (MSEa)
5b: SELENOMETHIONINE (MSEb)
5c: SELENOMETHIONINE (MSEc)
5d: SELENOMETHIONINE (MSEd)
5e: SELENOMETHIONINE (MSEe)
5f: SELENOMETHIONINE (MSEf)
5g: SELENOMETHIONINE (MSEg)
5h: SELENOMETHIONINE (MSEh)
5i: SELENOMETHIONINE (MSEi)
5j: SELENOMETHIONINE (MSEj)
5k: SELENOMETHIONINE (MSEk)
5l: SELENOMETHIONINE (MSEl)
5m: SELENOMETHIONINE (MSEm)
5n: SELENOMETHIONINE (MSEn)
5o: SELENOMETHIONINE (MSEo)
5p: SELENOMETHIONINE (MSEp)
5q: SELENOMETHIONINE (MSEq)
5r: SELENOMETHIONINE (MSEr)
5s: SELENOMETHIONINE (MSEs)
5t: SELENOMETHIONINE (MSEt)
6a: TETRAETHYLENE GLYCOL (PG4a)
7a: THIOCYANATE ION (SCNa)
7b: THIOCYANATE ION (SCNb)
7c: THIOCYANATE ION (SCNc)
7d: THIOCYANATE ION (SCNd)
7e: THIOCYANATE ION (SCNe)
7f: THIOCYANATE ION (SCNf)
7g: THIOCYANATE ION (SCNg)
7h: THIOCYANATE ION (SCNh)
7i: THIOCYANATE ION (SCNi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
BME
5
Ligand/Ion
BETA-MERCAPTOETHANOL
3
GOL
5
Ligand/Ion
GLYCEROL
4
MG
6
Ligand/Ion
MAGNESIUM ION
5
MSE
20
Mod. Amino Acid
SELENOMETHIONINE
6
PG4
1
Ligand/Ion
TETRAETHYLENE GLYCOL
7
SCN
9
Ligand/Ion
THIOCYANATE ION
[
close Hetero Component info
]
Sites
(28, 28)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:168 , ALA B:92 , PRO B:100 , HOH B:745
BINDING SITE FOR RESIDUE SCN B 1431
02
AC2
SOFTWARE
ARG A:228 , BME A:506 , HOH A:618
BINDING SITE FOR RESIDUE SCN A 1432
03
AC3
SOFTWARE
ALA B:224 , ARG B:228 , BME B:511 , HOH B:642
BINDING SITE FOR RESIDUE SCN B 1432
04
AC4
SOFTWARE
ARG A:302 , PG4 A:507
BINDING SITE FOR RESIDUE SCN A 1444
05
AC5
SOFTWARE
LYS A:399 , ARG B:62 , HOH B:1057 , HOH B:672
BINDING SITE FOR RESIDUE SCN B 1433
06
AC6
SOFTWARE
HOH A:937
BINDING SITE FOR RESIDUE SCN A 1433
07
AC7
SOFTWARE
ALA A:92 , PRO A:100 , HOH B:816 , LYS B:168
BINDING SITE FOR RESIDUE SCN A 1434
08
AC8
SOFTWARE
LEU A:7 , HOH A:645 , HOH A:999
BINDING SITE FOR RESIDUE SCN A 1435
09
AC9
SOFTWARE
PHE A:161 , GLN A:165 , GLY B:139 , LEU B:140 , HOH B:958
BINDING SITE FOR RESIDUE SCN A 1436
10
BC1
SOFTWARE
TYR A:136 , THR A:142 , ALA A:214 , ILE A:236 , GLY A:238 , LEU A:239 , GLY A:244 , PRO A:245 , ATP A:508
BINDING SITE FOR RESIDUE GOL A 1437
11
BC2
SOFTWARE
LEU B:189 , HIS B:356 , ILE B:416 , GLU B:417 , SER B:419 , HOH B:662 , HOH B:790 , HOH B:730 , HOH B:875
BINDING SITE FOR RESIDUE GOL B 1434
12
BC3
SOFTWARE
TYR B:136 , PHE B:141 , ALA B:214 , ILE B:236 , GLY B:238 , PRO B:245 , LYS B:422 , ATP B:512 , HOH B:904
BINDING SITE FOR RESIDUE GOL B 1435
13
BC4
SOFTWARE
HIS A:36 , PHE A:80 , ALA A:81 , VAL A:82 , ARG B:42 , GLU B:46 , HOH B:691
BINDING SITE FOR RESIDUE GOL B 1436
14
BC5
SOFTWARE
ARG A:41 , HOH A:737 , HIS B:36 , PHE B:80 , VAL B:82 , HOH B:742 , HOH B:601 , HOH B:605
BINDING SITE FOR RESIDUE GOL B 1437
15
BC6
SOFTWARE
ILE B:10 , ARG B:25 , ASP B:263 , HIS B:264 , ARG B:334 , HOH B:643
BINDING SITE FOR RESIDUE BME B 1438
16
BC7
SOFTWARE
PRO A:382 , THR B:313 , ARG B:315 , THR B:316 , HOH B:653
BINDING SITE FOR RESIDUE BME B 1439
17
BC8
SOFTWARE
GLY B:95 , GLY B:98 , LYS B:99 , PRO B:100
BINDING SITE FOR RESIDUE BME B 1440
18
BC9
SOFTWARE
ARG A:228 , CYS A:377 , SCN A:501
BINDING SITE FOR RESIDUE BME A 1438
19
CC1
SOFTWARE
ARG B:228 , CYS B:377 , PRO B:378 , SCN B:502
BINDING SITE FOR RESIDUE BME B 1441
20
CC2
SOFTWARE
ALA A:47 , SER A:61 , ARG A:62 , PHE A:63 , PRO A:64 , PHE A:65 , GLU A:276 , SCN A:512 , HOH A:805
BINDING SITE FOR RESIDUE PG4 A 1439
21
CC3
SOFTWARE
LYS A:68 , SER A:93 , SER A:94 , GLY A:95 , THR A:96 , THR A:97 , PHE A:141 , ALA A:214 , GLU A:215 , PRO A:216 , ASP A:235 , ILE A:236 , TYR A:237 , GLY A:238 , LEU A:239 , SER A:240 , ASP A:305 , ILE A:323 , ARG A:326 , LYS A:422 , GOL A:505 , MG A:509 , HOH A:638 , HOH A:702 , HOH A:663 , HOH A:776 , HOH A:735 , HOH A:720 , HOH A:833 , HOH A:650
BINDING SITE FOR RESIDUE ATP A 1440
22
CC4
SOFTWARE
LYS B:68 , SER B:93 , SER B:94 , GLY B:95 , THR B:96 , THR B:97 , PHE B:141 , ALA B:214 , GLU B:215 , PRO B:216 , ASP B:235 , ILE B:236 , TYR B:237 , GLY B:238 , LEU B:239 , SER B:240 , ASP B:305 , ILE B:323 , ARG B:326 , LYS B:422 , GOL B:505 , MG B:514 , HOH B:644 , HOH B:713 , HOH B:620 , HOH B:666 , HOH B:738 , HOH B:876 , HOH B:752 , HOH B:777
BINDING SITE FOR RESIDUE ATP B 1442
23
CC5
SOFTWARE
ATP A:508 , HOH A:638 , HOH A:702 , HOH A:735 , HOH A:720
BINDING SITE FOR RESIDUE MG A 1441
24
CC6
SOFTWARE
GLN B:350 , LEU B:353 , HOH B:654 , HOH B:869 , HOH B:871 , HOH B:642
BINDING SITE FOR RESIDUE MG B 1443
25
CC7
SOFTWARE
GLN A:350 , LEU A:353 , HOH A:848 , HOH A:713 , HOH A:635 , HOH A:618
BINDING SITE FOR RESIDUE MG A 1442
26
CC8
SOFTWARE
ATP B:512 , HOH B:620 , HOH B:666 , HOH B:752 , HOH B:777
BINDING SITE FOR RESIDUE MG B 1444
27
CC9
SOFTWARE
VAL B:203 , SER B:205 , LEU B:207 , MSE B:229 , GLY B:230
BINDING SITE FOR RESIDUE MG B 1445
28
DC1
SOFTWARE
VAL A:203 , SER A:205 , LEU A:207 , MSE A:229 , GLY A:230 , HOH A:960
BINDING SITE FOR RESIDUE MG A 1443
[
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
(1, 2)
Info
all PFAM domains
1a: PFAM_AMP_binding_2y27B01 (B:63-355)
1b: PFAM_AMP_binding_2y27B02 (B:63-355)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ANL
(32)
Family
:
AMP-binding
(32)
Burkholderia cepacia (strain J2315 / LMG 16656) (Burkholderia cenocepacia (strain J2315))
(3)
1a
AMP-binding-2y27B01
B:63-355
1b
AMP-binding-2y27B02
B:63-355
[
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 (168 KB)
Header - Asym.Unit
Biol.Unit 1 (159 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
2Y27
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help