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.
4G8J
Asym. Unit
Info
Asym.Unit (261 KB)
Biol.Unit 1 (255 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY STRUCTURE OF URIDINE PHOSPHORYLEASE FROM VIBRIO CHOLERAE COMPLEXED WITH THYMIDINE AT 2.12 A RESOLUTION
Authors
:
A. A. Lashkov, A. G. Gabdoulkhakov, I. I. Prokofev, S. E. Sotnichenko, C A. M. Mikhailov
Date
:
23 Jul 12 (Deposition) - 24 Jul 13 (Release) - 24 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.12
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Rossmann Fold, Alpha-Beta-Alpha Sandwich, Transferase, Nucleoside And Phosphate Binding, Phosphorylation, Cytosol
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. A. Lashkov, A. G. Gabdoulkhakov, I. I. Prokofev, S. E. Sotnichenko, C. Betzel, A. M. Mikhailov
X-Ray Structure Of Uridine Phosphorylease From Vibrio Cholerae Complexed With Thymidine
To Be Published
[
close entry info
]
Hetero Components
(5, 24)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
5a: THYMIDINE (THMa)
5b: THYMIDINE (THMb)
5c: THYMIDINE (THMc)
5d: THYMIDINE (THMd)
5e: THYMIDINE (THMe)
5f: THYMIDINE (THMf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
9
Ligand/Ion
CHLORIDE ION
2
EDO
4
Ligand/Ion
1,2-ETHANEDIOL
3
MG
2
Ligand/Ion
MAGNESIUM ION
4
NA
3
Ligand/Ion
SODIUM ION
5
THM
6
Ligand/Ion
THYMIDINE
[
close Hetero Component info
]
Sites
(24, 24)
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: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:93 , GLY A:95 , PHE A:161 , GLN A:165 , ARG A:167 , PHE A:194 , GLU A:195 , MET A:196 , GLU A:197 , ILE A:219 , ILE A:220 , HOH A:467 , HOH A:565 , HIS B:7 , ARG B:47
BINDING SITE FOR RESIDUE THM A 301
02
AC2
SOFTWARE
ASN A:221 , HOH A:488
BINDING SITE FOR RESIDUE CL A 302
03
AC3
SOFTWARE
GLY A:25 , ASP A:26 , ARG A:29
BINDING SITE FOR RESIDUE CL A 303
04
AC4
SOFTWARE
HOH A:573 , HOH A:574 , HOH A:575 , HOH A:576 , HOH A:577 , HOH A:578
BINDING SITE FOR RESIDUE MG A 304
05
AC5
SOFTWARE
HIS A:7 , ARG A:47 , HOH A:564 , THR B:93 , GLY B:95 , PHE B:161 , GLN B:165 , ARG B:167 , GLU B:195 , MET B:196 , GLU B:197 , ILE B:220 , HOH B:406 , HOH B:603
BINDING SITE FOR RESIDUE THM B 301
06
AC6
SOFTWARE
GLY B:25 , ASP B:26 , ARG B:29
BINDING SITE FOR RESIDUE CL B 302
07
AC7
SOFTWARE
GLU A:48 , ILE A:68 , SER A:72 , GLU B:48 , ILE B:68 , SER B:72
BINDING SITE FOR RESIDUE NA B 303
08
AC8
SOFTWARE
THR C:93 , GLY C:95 , PHE C:161 , GLN C:165 , ARG C:167 , GLU C:195 , MET C:196 , GLU C:197 , ILE C:220 , EDO C:304 , HOH C:620 , HIS D:7 , ARG D:47
BINDING SITE FOR RESIDUE THM C 301
09
AC9
SOFTWARE
TYR C:162 , ASP C:169 , HOH C:416 , PHE D:6 , GLN D:82
BINDING SITE FOR RESIDUE EDO C 302
10
BC1
SOFTWARE
ARG C:178 , HOH C:460 , HOH C:624 , LEU D:120
BINDING SITE FOR RESIDUE EDO C 303
11
BC2
SOFTWARE
PHE C:161 , THM C:301 , HOH C:657 , HIS D:7
BINDING SITE FOR RESIDUE EDO C 304
12
BC3
SOFTWARE
GLY C:25 , ASP C:26 , ARG C:29 , HOH D:456
BINDING SITE FOR RESIDUE CL C 305
13
BC4
SOFTWARE
GLU C:48 , ILE C:68 , SER C:72 , GLU D:48 , ILE D:68 , SER D:72
BINDING SITE FOR RESIDUE NA C 306
14
BC5
SOFTWARE
HIS C:7 , ARG C:47 , HOH C:495 , ILE D:68 , THR D:93 , GLY D:95 , PHE D:161 , GLN D:165 , ARG D:167 , GLU D:195 , MET D:196 , GLU D:197 , ILE D:220 , HOH D:589 , HOH D:626 , HOH D:631
BINDING SITE FOR RESIDUE THM D 301
15
BC6
SOFTWARE
HOH C:538 , GLY D:25 , ASP D:26 , ARG D:29 , HOH D:511
BINDING SITE FOR RESIDUE CL D 302
16
BC7
SOFTWARE
ILE E:68 , THR E:93 , PHE E:161 , GLN E:165 , ARG E:167 , PHE E:194 , GLU E:195 , MET E:196 , GLU E:197 , ILE E:220 , HOH E:494 , HOH E:568 , HOH E:584 , HIS F:7 , ARG F:47
BINDING SITE FOR RESIDUE THM E 301
17
BC8
SOFTWARE
ARG E:178 , HOH E:538 , HOH E:594 , LEU F:120 , HOH F:447
BINDING SITE FOR RESIDUE EDO E 302
18
BC9
SOFTWARE
GLY E:25 , ASP E:26 , HOH E:497
BINDING SITE FOR RESIDUE CL E 303
19
CC1
SOFTWARE
GLU E:48 , ILE E:68 , SER E:72 , GLU F:48 , ILE F:68 , SER F:72
BINDING SITE FOR RESIDUE NA E 304
20
CC2
SOFTWARE
HIS E:7 , ARG E:47 , THR F:93 , GLY F:95 , PHE F:161 , GLN F:165 , ARG F:167 , GLU F:195 , MET F:196 , GLU F:197 , ILE F:219 , ILE F:220 , HOH F:529
BINDING SITE FOR RESIDUE THM F 301
21
CC3
SOFTWARE
ASN F:221 , LYS F:225
BINDING SITE FOR RESIDUE CL F 302
22
CC4
SOFTWARE
GLY F:25 , ASP F:26
BINDING SITE FOR RESIDUE CL F 303
23
CC5
SOFTWARE
ARG F:174 , VAL F:175 , GLN F:180 , HOH F:491
BINDING SITE FOR RESIDUE CL F 304
24
CC6
SOFTWARE
HOH F:556 , HOH F:557 , HOH F:558 , HOH F:559 , HOH F:560 , HOH F:561
BINDING SITE FOR RESIDUE MG F 305
[
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, 6)
Info
All SCOP Domains
1a: SCOP_d4g8ja_ (A:)
1b: SCOP_d4g8je_ (E:)
1c: SCOP_d4g8jf_ (F:)
1d: SCOP_d4g8jb_ (B:)
1e: SCOP_d4g8jc_ (C:)
1f: SCOP_d4g8jd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Phosphorylase/hydrolase-like
(558)
Superfamily
:
Purine and uridine phosphorylases
(283)
Family
:
Purine and uridine phosphorylases
(224)
Protein domain
:
Uridine phosphorylase
(42)
Vibrio cholerae [TaxId: 243277]
(2)
1a
d4g8ja_
A:
1b
d4g8je_
E:
1c
d4g8jf_
F:
1d
d4g8jb_
B:
1e
d4g8jc_
C:
1f
d4g8jd_
D:
[
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 (261 KB)
Header - Asym.Unit
Biol.Unit 1 (255 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
4G8J
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
