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.
3D01
Biol. Unit 3
Info
Asym.Unit (622 KB)
Biol.Unit 1 (158 KB)
Biol.Unit 2 (156 KB)
Biol.Unit 3 (158 KB)
Biol.Unit 4 (156 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 THE PROTEIN ATU1372 WITH UNKNOWN FUNCTION FROM AGROBACTERIUM TUMEFACIENS
Authors
:
R. Zhang, X. Xu, J. Gu, A. Savchenko, A. M. Edwards, A. Joachimiak, Midwe For Structural Genomics (Mcsg)
Date
:
30 Apr 08 (Deposition) - 01 Jul 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,I,K (1x)
Biol. Unit 2: E,G,L (1x)
Biol. Unit 3: C,F,J (1x)
Biol. Unit 4: B,D,H (1x)
Keywords
:
Protein With Unknown Function, Structural Genomics, Psi, Mcsg, Protein Structure Initiative, Midwest Center For Structural Genomics, Unknown Function
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Zhang, X. Xu, J. Gu, A. Savchenko, A. M. Edwards, A. Joachimiak
The Crystal Structure Of The Protein Atu1372 With Unknown Function From Agrobacterium Tumefaciens.
To Be Published
[
close entry info
]
Hetero Components
(2, 13)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1aa: SELENOMETHIONINE (MSEaa)
1ab: SELENOMETHIONINE (MSEab)
1ac: SELENOMETHIONINE (MSEac)
1ad: SELENOMETHIONINE (MSEad)
1ae: SELENOMETHIONINE (MSEae)
1af: SELENOMETHIONINE (MSEaf)
1ag: SELENOMETHIONINE (MSEag)
1ah: SELENOMETHIONINE (MSEah)
1ai: SELENOMETHIONINE (MSEai)
1aj: SELENOMETHIONINE (MSEaj)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
1m: SELENOMETHIONINE (MSEm)
1n: SELENOMETHIONINE (MSEn)
1o: SELENOMETHIONINE (MSEo)
1p: SELENOMETHIONINE (MSEp)
1q: SELENOMETHIONINE (MSEq)
1r: SELENOMETHIONINE (MSEr)
1s: SELENOMETHIONINE (MSEs)
1t: SELENOMETHIONINE (MSEt)
1u: SELENOMETHIONINE (MSEu)
1v: SELENOMETHIONINE (MSEv)
1w: SELENOMETHIONINE (MSEw)
1x: SELENOMETHIONINE (MSEx)
1y: SELENOMETHIONINE (MSEy)
1z: SELENOMETHIONINE (MSEz)
2a: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-... (PG5a)
2b: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-... (PG5b)
2c: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-... (PG5c)
2d: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-... (PG5d)
2e: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-... (PG5e)
2f: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-... (PG5f)
2g: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-... (PG5g)
2h: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-... (PG5h)
2i: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-... (PG5i)
2j: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-... (PG5j)
2k: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-... (PG5k)
2l: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-... (PG5l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
9
Mod. Amino Acid
SELENOMETHIONINE
2
PG5
4
Ligand/Ion
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC7 (SOFTWARE)
3: AC8 (SOFTWARE)
4: AC9 (SOFTWARE)
5: BC1 (SOFTWARE)
6: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU D:114 , ARG F:66 , ASP H:67 , ASN H:152
BINDING SITE FOR RESIDUE PG5 H 166
2
AC7
SOFTWARE
THR B:61 , ASN B:152 , ARG C:66
BINDING SITE FOR RESIDUE PG5 B 166
3
AC8
SOFTWARE
ARG B:66 , THR C:61 , GLY C:62 , ASP C:67 , ASN C:152 , GLU J:114
BINDING SITE FOR RESIDUE PG5 C 166
4
AC9
SOFTWARE
THR F:61 , ASP F:67 , ASN F:152 , ARG H:66
BINDING SITE FOR RESIDUE PG5 F 166
5
BC1
SOFTWARE
ARG D:66 , ASN J:152
BINDING SITE FOR RESIDUE PG5 J 166
6
BC2
SOFTWARE
GLU B:114 , GLY D:62 , ASP D:67 , ASN D:152 , ARG J:66
BINDING SITE FOR RESIDUE PG5 J 167
[
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
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d3d01a_ (A:)
1b: SCOP_d3d01b_ (B:)
1c: SCOP_d3d01k_ (K:)
1d: SCOP_d3d01l_ (L:)
1e: SCOP_d3d01c_ (C:)
1f: SCOP_d3d01d_ (D:)
1g: SCOP_d3d01e_ (E:)
1h: SCOP_d3d01f_ (F:)
1i: SCOP_d3d01g_ (G:)
1j: SCOP_d3d01h_ (H:)
1k: SCOP_d3d01i_ (I:)
1l: SCOP_d3d01j_ (J:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Bacillus chorismate mutase-like
(324)
Superfamily
:
YjgF-like
(45)
Family
:
automated matches
(12)
Protein domain
:
automated matches
(12)
Agrobacterium tumefaciens [TaxId: 176299]
(1)
1a
d3d01a_
A:
1b
d3d01b_
B:
1c
d3d01k_
K:
1d
d3d01l_
L:
1e
d3d01c_
C:
1f
d3d01d_
D:
1g
d3d01e_
E:
1h
d3d01f_
F:
1i
d3d01g_
G:
1j
d3d01h_
H:
1k
d3d01i_
I:
1l
d3d01j_
J:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_3d01E00 (E:4-164)
1b: CATH_3d01D00 (D:3-163)
1c: CATH_3d01I00 (I:2-164)
1d: CATH_3d01L00 (L:2-165)
1e: CATH_3d01B00 (B:4-165)
1f: CATH_3d01C00 (C:3-164)
1g: CATH_3d01G00 (G:2-163)
1h: CATH_3d01H00 (H:3-164)
1i: CATH_3d01J00 (J:3-164)
1j: CATH_3d01K00 (K:2-165)
1k: CATH_3d01A00 (A:1-163)
1l: CATH_3d01F00 (F:2-164)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
60s Ribosomal Protein L30; Chain: A;
(235)
Homologous Superfamily
:
[code=3.30.1330.40, no name defined]
(35)
C58 (Agrobacterium tumefaciens str)
(1)
1a
3d01E00
E:4-164
1b
3d01D00
D:3-163
1c
3d01I00
I:2-164
1d
3d01L00
L:2-165
1e
3d01B00
B:4-165
1f
3d01C00
C:3-164
1g
3d01G00
G:2-163
1h
3d01H00
H:3-164
1i
3d01J00
J:3-164
1j
3d01K00
K:2-165
1k
3d01A00
A:1-163
1l
3d01F00
F:2-164
[
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 C
Chain F
Chain J
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 (622 KB)
Header - Asym.Unit
Biol.Unit 1 (158 KB)
Header - Biol.Unit 1
Biol.Unit 2 (156 KB)
Header - Biol.Unit 2
Biol.Unit 3 (158 KB)
Header - Biol.Unit 3
Biol.Unit 4 (156 KB)
Header - Biol.Unit 4
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
3D01
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help