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.
4N9A
Asym. Unit
Info
Asym.Unit (130 KB)
Biol.Unit 1 (124 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
E. COLI SLIDING CLAMP IN COMPLEX WITH (R)-6-CHLORO-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-1-CARBOXYLIC ACID
Authors
:
Z. Yin, A. J. Oakley
Date
:
19 Oct 13 (Deposition) - 06 Nov 13 (Release) - 09 Apr 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Poliii Beta, Sliding Clamp, Dnan, Transferase-Transferase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Yin, L. R. Whittell, Y. Wang, S. Jergic, M. Liu, E. J. Harry, N. E. Dixon, J. L. Beck, M. J. Kelso, A. J. Oakley
Discovery Of Lead Compounds Targeting The Bacterial Sliding Clamp Using A Fragment-Based Approach.
J. Med. Chem. V. 57 2799 2014
[
close entry info
]
Hetero Components
(5, 11)
Info
All Hetero Components
1a: (1R)-6-CHLORO-2,3,4,9-TETRAHYDRO-1... (2J2a)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
5a: TETRAETHYLENE GLYCOL (PG4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2J2
1
Ligand/Ion
(1R)-6-CHLORO-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-1-CARBOXYLIC ACID
2
CA
5
Ligand/Ion
CALCIUM ION
3
CL
2
Ligand/Ion
CHLORIDE ION
4
PEG
2
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PG4
1
Ligand/Ion
TETRAETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH B:641
BINDING SITE FOR RESIDUE CA A 401
02
AC2
SOFTWARE
ASP A:121 , TRP A:122 , ARG A:224 , SER B:43 , HOH B:567
BINDING SITE FOR RESIDUE PG4 A 402
03
AC3
SOFTWARE
GLY A:280 , ALA A:294 , ASN A:295 , HOH A:600
BINDING SITE FOR RESIDUE CA A 403
04
AC4
SOFTWARE
THR A:172 , GLY A:174 , ARG A:176 , PRO A:242 , VAL A:247 , MET A:362
BINDING SITE FOR RESIDUE 2J2 A 404
05
AC5
SOFTWARE
SER A:345 , HOH A:529 , HOH A:673 , GLU B:163 , GLU B:166 , ARG B:168 , HOH B:638 , HOH B:674
BINDING SITE FOR RESIDUE PEG A 405
06
AC6
SOFTWARE
ALA A:114 , PHE A:116 , PRO A:117 , ASN A:118
BINDING SITE FOR RESIDUE PEG A 406
07
AC7
SOFTWARE
SER A:181 , HOH A:621
BINDING SITE FOR RESIDUE CL A 407
08
AC8
SOFTWARE
THR A:4 , VAL A:5 , LEU A:59 , VAL A:60 , GLN A:61 , HOH A:518 , HOH A:519
BINDING SITE FOR RESIDUE CL A 408
09
AC9
SOFTWARE
ASP B:211
BINDING SITE FOR RESIDUE CA B 401
10
BC1
SOFTWARE
GLY B:46 , GLU B:202
BINDING SITE FOR RESIDUE CA B 402
11
BC2
SOFTWARE
THR A:341 , HOH A:578 , HOH A:719 , HOH B:533 , HOH B:580
BINDING SITE FOR RESIDUE CA B 403
[
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, 6)
Info
All SCOP Domains
1a: SCOP_d4n9aa1 (A:1-122)
1b: SCOP_d4n9aa2 (A:123-244)
1c: SCOP_d4n9aa3 (A:245-364)
1d: SCOP_d4n9ab1 (B:1-122)
1e: SCOP_d4n9ab2 (B:123-244)
1f: SCOP_d4n9ab3 (B:245-366)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
DNA clamp
(88)
Superfamily
:
DNA clamp
(88)
Family
:
DNA polymerase III, beta subunit
(31)
Protein domain
:
DNA polymerase III, beta subunit
(31)
Escherichia coli [TaxId: 562]
(30)
1a
d4n9aa1
A:1-122
1b
d4n9aa2
A:123-244
1c
d4n9aa3
A:245-364
1d
d4n9ab1
B:1-122
1e
d4n9ab2
B:123-244
1f
d4n9ab3
B:245-366
[
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 (130 KB)
Header - Asym.Unit
Biol.Unit 1 (124 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
4N9A
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help