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.
1RWI
Biol. Unit 1
Info
Asym.Unit (88 KB)
Biol.Unit 1 (43 KB)
Biol.Unit 2 (43 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
EXTRACELLULAR DOMAIN OF MYCOBACTERIUM TUBERCULOSIS PKND
Authors
:
M. C. Good, A. E. Greenstein, T. A. Young, H. L. Ng, T. Alber, Tb Structural Genomics Consortium (Tbsgc)
Date
:
16 Dec 03 (Deposition) - 27 Apr 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: B (1x)
Biol. Unit 2: A (1x)
Keywords
:
Beta Propeller, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. C. Good, A. E. Greenstein, T. A. Young, H. L. Ng, T. Alber
Sensor Domain Of The Mycobacterium Tuberculosis Receptor Ser/Thr Protein Kinase, Pknd, Forms A Highly Symmetric Beta Propeller.
J. Mol. Biol. V. 339 459 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
1c: CADMIUM ION (CDc)
1d: CADMIUM ION (CDd)
1e: CADMIUM ION (CDe)
1f: CADMIUM ION (CDf)
1g: CADMIUM ION (CDg)
1h: CADMIUM ION (CDh)
1i: CADMIUM ION (CDi)
1j: CADMIUM ION (CDj)
1k: CADMIUM ION (CDk)
1l: CADMIUM ION (CDl)
1m: CADMIUM ION (CDm)
1n: CADMIUM ION (CDn)
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC4 (SOFTWARE)
04: AC5 (SOFTWARE)
05: AC6 (SOFTWARE)
06: AC7 (SOFTWARE)
07: AC8 (SOFTWARE)
08: AC9 (SOFTWARE)
09: BC1 (SOFTWARE)
10: BC2 (SOFTWARE)
11: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:264 , HIS A:267 , ASP B:151 , HOH B:1304 , HOH B:1322
BINDING SITE FOR RESIDUE CD A 1001
02
AC3
SOFTWARE
HIS A:268 , HIS A:269 , HIS A:270 , GLU B:42 , HOH B:1306 , HOH B:1365
BINDING SITE FOR RESIDUE CD A 1003
03
AC4
SOFTWARE
ASP A:244 , HOH A:1229 , ASP B:169
BINDING SITE FOR RESIDUE CD B 1004
04
AC5
SOFTWARE
ASP A:169 , ASP B:244 , HIS B:269 , HOH B:1354 , HOH B:1370
BINDING SITE FOR RESIDUE CD B 1101
05
AC6
SOFTWARE
ASP A:151 , GLU B:264 , HIS B:267 , HOH B:1312 , HOH B:1320
BINDING SITE FOR RESIDUE CD B 1102
06
AC7
SOFTWARE
HIS B:265 , HIS B:266
BINDING SITE FOR RESIDUE CD B 1103
07
AC8
SOFTWARE
GLU A:42 , HIS B:268 , HIS B:270 , HOH B:1314 , HOH B:1351
BINDING SITE FOR RESIDUE CD B 1104
08
AC9
SOFTWARE
HIS A:270 , GLU B:111 , ASP B:153
BINDING SITE FOR RESIDUE CD B 1201
09
BC1
SOFTWARE
HIS A:269 , HIS B:210
BINDING SITE FOR RESIDUE CD A 1202
10
BC2
SOFTWARE
ASN B:150 , ASP B:151 , ASP B:169 , HOH B:1356
BINDING SITE FOR RESIDUE CD B 1203
11
BC4
SOFTWARE
HIS B:269
BINDING SITE FOR RESIDUE CD B 1302
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 12)
Info
All PROSITE Patterns/Profiles
1: NHL (B:180-221)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NHL
PS51125
NHL repeat profile.
PKND_MYCTO
414-456
498-539
461-497
540-581
624-664
582-623
6
-
B:12-52
-
B:96-137
-
B:59-95
-
B:138-179
-
B:222-262
-
B:180-221
PKND_MYCTU
414-456
498-539
461-497
540-581
624-664
582-623
6
-
B:12-52
-
B:96-137
-
B:59-95
-
B:138-179
-
B:222-262
-
B:180-221
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1rwia_ (A:)
1b: SCOP_d1rwib_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
6-bladed beta-propeller
(327)
Superfamily
:
NHL repeat
(3)
Family
:
NHL repeat
(3)
Protein domain
:
Serine/threonine-protein kinase PknD
(2)
Mycobacterium tuberculosis [TaxId: 1773]
(2)
1a
d1rwia_
A:
1b
d1rwib_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1rwiA00 (A:11-270)
1b: CATH_1rwiB00 (B:12-270)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
6 Propellor
(215)
Topology
:
Neuraminidase
(215)
Homologous Superfamily
:
TolB, C-terminal domain
(42)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(2)
1a
1rwiA00
A:11-270
1b
1rwiB00
B:12-270
[
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 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 (88 KB)
Header - Asym.Unit
Biol.Unit 1 (43 KB)
Header - Biol.Unit 1
Biol.Unit 2 (43 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
1RWI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help