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.
5X22
Asym. Unit
Info
Asym.Unit (1.1 MB)
Biol.Unit 1 (579 KB)
Biol.Unit 2 (591 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 THERMUS THERMOPHILUS TRANSCRIPTION INITIATION COMPLEX WITH GPA AND CMPCPP
Authors
:
Y. Zhang, R. Ebright
Date
:
29 Jan 17 (Deposition) - 05 Jul 17 (Release) - 05 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.35
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S
Biol. Unit 1: A,B,C,D,E,F,G,H,I (1x)
Biol. Unit 2: K,L,M,N,O,P,Q,R,S (1x)
Keywords
:
Transcription, Rna Polymerase, Primer-Dependent Initiation, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. I. Maffioli, Y. Zhang, D. Degen, T. Carzaniga, G. Del Gatto, S. Serina, P. Monciardini, C. Mazzetti, P. Guglierame, G. Candiani, A. I. Chiriac, G. Facchetti, P. Kaltofen, H. G. Sahl, G. Deho, S. Donadio, R. H. Ebright
Antibacterial Nucleoside-Analog Inhibitor Of Bacterial Rna Polymerase.
Cell V. 169 1240 2017
[
close entry info
]
Hetero Components
(3, 18)
Info
All Hetero Components
1a: 5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHO... (2TMa)
1b: 5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHO... (2TMb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
2j: MAGNESIUM ION (MGj)
2k: MAGNESIUM ION (MGk)
2l: MAGNESIUM ION (MGl)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2TM
2
Ligand/Ion
5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE
2
MG
12
Ligand/Ion
MAGNESIUM ION
3
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(18, 18)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP B:183 , ASP B:191 , LEU B:192 , ASP B:193
binding site for residue MG B 2001
02
AC2
SOFTWARE
CYS D:1112 , CYS D:1194 , CYS D:1201 , CYS D:1204
binding site for residue ZN D 2001
03
AC3
SOFTWARE
CYS D:58 , CYS D:60 , CYS D:73 , CYS D:76
binding site for residue ZN D 2002
04
AC4
SOFTWARE
ASP D:739 , ASP D:741 , ASP D:743 , A I:2
binding site for residue MG D 2003
05
AC5
SOFTWARE
ASP D:739 , 2TM D:2007
binding site for residue MG D 2004
06
AC6
SOFTWARE
ASP B:168 , LYS D:840
binding site for residue MG D 2005
07
AC7
SOFTWARE
TRP D:897 , GLU D:898 , ILE D:900
binding site for residue MG D 2006
08
AC8
SOFTWARE
ARG C:557 , ARG C:879 , ARG D:704 , PRO D:706 , ASN D:737 , ASP D:739 , ARG D:783 , ARG D:1029 , GLN D:1235 , MET D:1238 , ARG D:1239 , THR D:1240 , MG D:2004 , DG G:14 , A I:2
binding site for residue 2TM D 2007
09
AC9
SOFTWARE
ALA F:292 , GLY F:296 , TRP F:299
binding site for residue MG F 2001
10
AD1
SOFTWARE
ASP L:183 , ASP L:191 , LEU L:192 , ASP L:193
binding site for residue MG L 2001
11
AD2
SOFTWARE
CYS N:1112 , CYS N:1194 , CYS N:1201 , CYS N:1204
binding site for residue ZN N 2001
12
AD3
SOFTWARE
CYS N:58 , CYS N:60 , CYS N:73 , CYS N:76
binding site for residue ZN N 2002
13
AD4
SOFTWARE
ASP N:739 , ASP N:741 , ASP N:743 , A S:2
binding site for residue MG N 2003
14
AD5
SOFTWARE
ARG M:879 , ASP N:739 , 2TM N:2007
binding site for residue MG N 2004
15
AD6
SOFTWARE
ASP L:168 , LYS N:840
binding site for residue MG N 2005
16
AD7
SOFTWARE
TRP N:897 , GLU N:898 , ILE N:900
binding site for residue MG N 2006
17
AD8
SOFTWARE
ARG M:557 , ARG M:879 , ARG N:704 , PRO N:706 , ASN N:737 , ASP N:739 , ARG N:1029 , GLN N:1235 , MET N:1238 , ARG N:1239 , MG N:2004 , DG Q:14 , A S:2
binding site for residue 2TM N 2007
18
AD9
SOFTWARE
ALA P:292 , GLY P:296 , TRP P:299
binding site for residue MG P 2001
[
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
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
Chain Q
Chain R
Chain S
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 (1.1 MB)
Header - Asym.Unit
Biol.Unit 1 (579 KB)
Header - Biol.Unit 1
Biol.Unit 2 (591 KB)
Header - Biol.Unit 2
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
5X22
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
