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.
3K4G
Asym. Unit
Info
Asym.Unit (123 KB)
Biol.Unit 1 (18 KB)
Biol.Unit 2 (18 KB)
Biol.Unit 3 (18 KB)
Biol.Unit 4 (18 KB)
Biol.Unit 5 (17 KB)
Biol.Unit 6 (18 KB)
Biol.Unit 7 (18 KB)
Biol.Unit 8 (17 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 E. COLI RNA POLYMERASE ALPHA SUBUNIT C-TERMINAL DOMAIN
Authors
:
S. Lara-Gonzalez, J. Birktoft, C. L. Lawson
Date
:
05 Oct 09 (Deposition) - 07 Jul 10 (Release) - 07 Sep 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Keywords
:
Bacterial Transcription Regulation, Dna-Directed Rna Polymerase, Nucleotidyltransferase, Transcription, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Lara-Gonzalez, J. J. Birktoft, C. L. Lawson
Structure Of The Escherichia Coli Rna Polymerase Alpha Subunit C-Terminal Domain.
Acta Crystallogr. , Sect. D V. 66 806 2010
[
close entry info
]
Hetero Components
(2, 52)
Info
All Hetero Components
1a: N-DIMETHYL-LYSINE (MLYa)
1aa: N-DIMETHYL-LYSINE (MLYaa)
1ab: N-DIMETHYL-LYSINE (MLYab)
1ac: N-DIMETHYL-LYSINE (MLYac)
1ad: N-DIMETHYL-LYSINE (MLYad)
1ae: N-DIMETHYL-LYSINE (MLYae)
1af: N-DIMETHYL-LYSINE (MLYaf)
1ag: N-DIMETHYL-LYSINE (MLYag)
1ah: N-DIMETHYL-LYSINE (MLYah)
1ai: N-DIMETHYL-LYSINE (MLYai)
1aj: N-DIMETHYL-LYSINE (MLYaj)
1ak: N-DIMETHYL-LYSINE (MLYak)
1al: N-DIMETHYL-LYSINE (MLYal)
1am: N-DIMETHYL-LYSINE (MLYam)
1an: N-DIMETHYL-LYSINE (MLYan)
1ao: N-DIMETHYL-LYSINE (MLYao)
1ap: N-DIMETHYL-LYSINE (MLYap)
1aq: N-DIMETHYL-LYSINE (MLYaq)
1ar: N-DIMETHYL-LYSINE (MLYar)
1as: N-DIMETHYL-LYSINE (MLYas)
1at: N-DIMETHYL-LYSINE (MLYat)
1au: N-DIMETHYL-LYSINE (MLYau)
1av: N-DIMETHYL-LYSINE (MLYav)
1b: N-DIMETHYL-LYSINE (MLYb)
1c: N-DIMETHYL-LYSINE (MLYc)
1d: N-DIMETHYL-LYSINE (MLYd)
1e: N-DIMETHYL-LYSINE (MLYe)
1f: N-DIMETHYL-LYSINE (MLYf)
1g: N-DIMETHYL-LYSINE (MLYg)
1h: N-DIMETHYL-LYSINE (MLYh)
1i: N-DIMETHYL-LYSINE (MLYi)
1j: N-DIMETHYL-LYSINE (MLYj)
1k: N-DIMETHYL-LYSINE (MLYk)
1l: N-DIMETHYL-LYSINE (MLYl)
1m: N-DIMETHYL-LYSINE (MLYm)
1n: N-DIMETHYL-LYSINE (MLYn)
1o: N-DIMETHYL-LYSINE (MLYo)
1p: N-DIMETHYL-LYSINE (MLYp)
1q: N-DIMETHYL-LYSINE (MLYq)
1r: N-DIMETHYL-LYSINE (MLYr)
1s: N-DIMETHYL-LYSINE (MLYs)
1t: N-DIMETHYL-LYSINE (MLYt)
1u: N-DIMETHYL-LYSINE (MLYu)
1v: N-DIMETHYL-LYSINE (MLYv)
1w: N-DIMETHYL-LYSINE (MLYw)
1x: N-DIMETHYL-LYSINE (MLYx)
1y: N-DIMETHYL-LYSINE (MLYy)
1z: N-DIMETHYL-LYSINE (MLYz)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
2d: SODIUM ION (NAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MLY
48
Mod. Amino Acid
N-DIMETHYL-LYSINE
2
NA
4
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:320 , PRO A:322 , ASN B:320 , PRO B:322 , HOH C:107
BINDING SITE FOR RESIDUE NA A 2
2
AC2
SOFTWARE
HOH B:204 , ASN C:320 , PRO C:322 , ASN D:320 , PRO D:322
BINDING SITE FOR RESIDUE NA C 4
3
AC3
SOFTWARE
ASN E:320 , PRO E:322 , ASN F:320 , PRO F:322 , HOH G:331
BINDING SITE FOR RESIDUE NA E 3
4
AC4
SOFTWARE
ASN G:320 , PRO G:322 , ASN H:320 , PRO H:322
BINDING SITE FOR RESIDUE NA G 1
[
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, 8)
Info
All SCOP Domains
1a: SCOP_d3k4ga_ (A:)
1b: SCOP_d3k4gb_ (B:)
1c: SCOP_d3k4gc_ (C:)
1d: SCOP_d3k4gd_ (D:)
1e: SCOP_d3k4ge_ (E:)
1f: SCOP_d3k4gf_ (F:)
1g: SCOP_d3k4gg_ (G:)
1h: SCOP_d3k4gh_ (H:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
SAM domain-like
(639)
Superfamily
:
C-terminal domain of RNA polymerase alpha subunit
(9)
Family
:
C-terminal domain of RNA polymerase alpha subunit
(9)
Protein domain
:
automated matches
(4)
Escherichia coli K-12 [TaxId: 83333]
(2)
1a
d3k4ga_
A:
1b
d3k4gb_
B:
1c
d3k4gc_
C:
1d
d3k4gd_
D:
1e
d3k4ge_
E:
1f
d3k4gf_
F:
1g
d3k4gg_
G:
1h
d3k4gh_
H:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_RNA_pol_A_CTD_3k4gH01 (H:246-309)
1b: PFAM_RNA_pol_A_CTD_3k4gH02 (H:246-309)
1c: PFAM_RNA_pol_A_CTD_3k4gH03 (H:246-309)
1d: PFAM_RNA_pol_A_CTD_3k4gH04 (H:246-309)
1e: PFAM_RNA_pol_A_CTD_3k4gH05 (H:246-309)
1f: PFAM_RNA_pol_A_CTD_3k4gH06 (H:246-309)
1g: PFAM_RNA_pol_A_CTD_3k4gH07 (H:246-309)
1h: PFAM_RNA_pol_A_CTD_3k4gH08 (H:246-309)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: RNA_pol_A_CTD]
(7)
Family
:
RNA_pol_A_CTD
(7)
Escherichia coli (strain K12)
(5)
1a
RNA_pol_A_CTD-3k4gH01
H:246-309
1b
RNA_pol_A_CTD-3k4gH02
H:246-309
1c
RNA_pol_A_CTD-3k4gH03
H:246-309
1d
RNA_pol_A_CTD-3k4gH04
H:246-309
1e
RNA_pol_A_CTD-3k4gH05
H:246-309
1f
RNA_pol_A_CTD-3k4gH06
H:246-309
1g
RNA_pol_A_CTD-3k4gH07
H:246-309
1h
RNA_pol_A_CTD-3k4gH08
H:246-309
[
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
Chain D
Chain E
Chain F
Chain G
Chain H
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 (123 KB)
Header - Asym.Unit
Biol.Unit 1 (18 KB)
Header - Biol.Unit 1
Biol.Unit 2 (18 KB)
Header - Biol.Unit 2
Biol.Unit 3 (18 KB)
Header - Biol.Unit 3
Biol.Unit 4 (18 KB)
Header - Biol.Unit 4
Biol.Unit 5 (17 KB)
Header - Biol.Unit 5
Biol.Unit 6 (18 KB)
Header - Biol.Unit 6
Biol.Unit 7 (18 KB)
Header - Biol.Unit 7
Biol.Unit 8 (17 KB)
Header - Biol.Unit 8
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
3K4G
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
