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.
3B4T
Asym. Unit
Info
Asym.Unit (245 KB)
Biol.Unit 1 (239 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 MYCOBACTERIUM TUBERCULOSIS RNASE PH, THE MYCOBACTERIUM TUBERCULOSIS STRUCTURAL GENOMICS CONSORTIUM TARGET RV1340
Authors
:
A. J. Antczak, J. M. Berger, T. Lekin, B. W. Segelke, Mycobacterium Tub Structural Genomics Consortium (Tbsgc), Tb Structural Genomi Consortium (Tbsgc)
Date
:
24 Oct 07 (Deposition) - 20 Nov 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Rnase, Trna Nucleotidyltransferase, Ribonuclease, Rpha, Structural Genomics, Tbsgc, Mycobacterium Tuberculosis Structural Genomics Consortium, Trna Processing, Tb Structural Genomics Consortium, Psi, Protein Structure Initiative, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. J. Antczak, T. Lekin, B. W. Segelke, J. M. Berger
2. 1 A Crystal Structure Of Rnase Ph From Mycobacterium Tuberculosis.
To Be Published
[
close entry info
]
Hetero Components
(1, 10)
Info
All Hetero Components
1a: PHOSPHATE ION (PO4a)
1b: PHOSPHATE ION (PO4b)
1c: PHOSPHATE ION (PO4c)
1d: PHOSPHATE ION (PO4d)
1e: PHOSPHATE ION (PO4e)
1f: PHOSPHATE ION (PO4f)
1g: PHOSPHATE ION (PO4g)
1h: PHOSPHATE ION (PO4h)
1i: PHOSPHATE ION (PO4i)
1j: PHOSPHATE ION (PO4j)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PO4
10
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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
(1, 6)
Info
All PROSITE Patterns/Profiles
1: RIBONUCLEASE_PH (A:117-130,B:117-130,C:117-130,D:11...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBONUCLEASE_PH
PS01277
Ribonuclease PH signature.
RNPH_MYCTO
118-131
6
A:117-130
B:117-130
C:117-130
D:117-130
E:117-130
F:117-130
RNPH_MYCTU
118-131
6
A:117-130
B:117-130
C:117-130
D:117-130
E:117-130
F:117-130
[
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
(2, 12)
Info
All SCOP Domains
1a: SCOP_d3b4ta2 (A:152-247)
1b: SCOP_d3b4tb2 (B:152-247)
1c: SCOP_d3b4tc2 (C:152-247)
1d: SCOP_d3b4td2 (D:152-247)
1e: SCOP_d3b4te2 (E:152-247)
1f: SCOP_d3b4tf2 (F:152-247)
2a: SCOP_d3b4ta1 (A:1-151)
2b: SCOP_d3b4tb1 (B:2-151)
2c: SCOP_d3b4tc1 (C:2-151)
2d: SCOP_d3b4td1 (D:2-151)
2e: SCOP_d3b4te1 (E:1-151)
2f: SCOP_d3b4tf1 (F:1-151)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ribonuclease PH domain 2-like
(52)
Superfamily
:
Ribonuclease PH domain 2-like
(52)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Mycobacterium tuberculosis [TaxId: 83332]
(1)
1a
d3b4ta2
A:152-247
1b
d3b4tb2
B:152-247
1c
d3b4tc2
C:152-247
1d
d3b4td2
D:152-247
1e
d3b4te2
E:152-247
1f
d3b4tf2
F:152-247
Fold
:
Ribosomal protein S5 domain 2-like
(306)
Superfamily
:
Ribosomal protein S5 domain 2-like
(306)
Family
:
automated matches
(39)
Protein domain
:
automated matches
(39)
Mycobacterium tuberculosis [TaxId: 83332]
(3)
2a
d3b4ta1
A:1-151
2b
d3b4tb1
B:2-151
2c
d3b4tc1
C:2-151
2d
d3b4td1
D:2-151
2e
d3b4te1
E:1-151
2f
d3b4tf1
F:1-151
[
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
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 (245 KB)
Header - Asym.Unit
Biol.Unit 1 (239 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
3B4T
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help