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.
4OGL
Asym. Unit
Info
Asym.Unit (604 KB)
Biol.Unit 1 (598 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 URIDINE PHOSPHORYLASE FROM VIBRIO CHOLERAE IN COMPLEX WITH THYMINE AT 1.25 A RESOLUTION
Authors
:
I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, C. Betzel, A. M. Mikh
Date
:
16 Jan 14 (Deposition) - 04 Mar 15 (Release) - 11 Jan 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.25
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Rossmann Fold, Transferase, Nucleoside, Phosphate Ion
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, T. Balaev, A. S. Seregina, C. Mironov, C. Betzel, A. M. Mikhailov
X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae In Complex With Thymine At 1. 25 A Resolution
Crystallogr. Rep. 2016
[
close entry info
]
Hetero Components
(5, 25)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
4a: THYMINE (TDRa)
4b: THYMINE (TDRb)
4c: THYMINE (TDRc)
4d: THYMINE (TDRd)
4e: THYMINE (TDRe)
4f: THYMINE (TDRf)
5a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
9
Ligand/Ion
1,2-ETHANEDIOL
2
GOL
6
Ligand/Ion
GLYCEROL
3
NA
3
Ligand/Ion
SODIUM ION
4
TDR
6
Ligand/Ion
THYMINE
5
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(25, 25)
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)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:93 , THR A:94 , GLY A:95 , PHE A:161 , GLN A:165 , ARG A:167 , GLU A:195 , MET A:196 , ILE A:219 , ILE A:220 , GOL A:303 , HOH A:402
BINDING SITE FOR RESIDUE TDR A 301
02
AC2
SOFTWARE
ARG A:178 , HOH A:408 , HOH A:409 , HOH A:603 , HOH A:674 , HOH A:721 , LEU B:120 , HOH F:626
BINDING SITE FOR RESIDUE EDO A 302
03
AC3
SOFTWARE
GLU A:197 , TDR A:301 , HOH A:459 , HOH A:503 , HOH A:527 , HOH A:723 , HIS B:7
BINDING SITE FOR RESIDUE GOL A 303
04
AC4
SOFTWARE
GLU A:48 , ILE A:68 , SER A:72 , GLU B:48 , ILE B:68 , SER B:72
BINDING SITE FOR RESIDUE NA A 304
05
AC5
SOFTWARE
GLY B:95 , PHE B:161 , GLN B:165 , ARG B:167 , GLU B:195 , MET B:196 , ILE B:220 , TRS B:303 , HOH B:418 , HOH B:732
BINDING SITE FOR RESIDUE TDR B 301
06
AC6
SOFTWARE
PHE B:6 , HIS B:7 , GLY B:9 , HIS B:46 , HOH B:711
BINDING SITE FOR RESIDUE EDO B 302
07
AC7
SOFTWARE
HIS A:7 , ARG A:47 , ILE B:68 , THR B:93 , GLU B:195 , MET B:196 , GLU B:197 , TDR B:301 , HOH B:467 , HOH B:509
BINDING SITE FOR RESIDUE TRS B 303
08
AC8
SOFTWARE
THR C:94 , GLY C:95 , PHE C:161 , GLN C:165 , ARG C:167 , PHE C:194 , GLU C:195 , MET C:196 , ILE C:220 , GOL C:305 , HOH C:408
BINDING SITE FOR RESIDUE TDR C 301
09
AC9
SOFTWARE
HOH B:724 , ARG C:178 , HOH C:414 , HOH C:417 , HOH C:643 , HOH C:649 , HOH C:683 , LEU D:120
BINDING SITE FOR RESIDUE EDO C 302
10
BC1
SOFTWARE
ASP C:132 , HOH C:407 , HOH C:426 , HOH C:554 , HOH C:766
BINDING SITE FOR RESIDUE EDO C 303
11
BC2
SOFTWARE
LYS C:3 , GLN C:82 , HOH C:674 , ASP D:169 , THR D:170 , PHE D:171 , HOH D:544
BINDING SITE FOR RESIDUE EDO C 304
12
BC3
SOFTWARE
PHE C:161 , GLU C:197 , TDR C:301 , HOH C:476 , HOH C:491 , HIS D:7
BINDING SITE FOR RESIDUE GOL 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
THR D:94 , GLY D:95 , PHE D:161 , GLN D:165 , ARG D:167 , GLU D:195 , MET D:196 , ILE D:220 , GOL D:302 , HOH D:409
BINDING SITE FOR RESIDUE TDR D 301
15
BC6
SOFTWARE
HIS C:7 , ARG C:47 , ILE D:68 , PHE D:161 , GLU D:197 , TDR D:301 , GOL D:303 , HOH D:452 , HOH D:468
BINDING SITE FOR RESIDUE GOL D 302
16
BC7
SOFTWARE
ARG C:47 , HOH C:791 , PHE D:161 , GLU D:226 , GOL D:302
BINDING SITE FOR RESIDUE GOL D 303
17
BC8
SOFTWARE
GLY E:95 , PHE E:161 , GLN E:165 , ARG E:167 , GLU E:195 , MET E:196 , ILE E:220 , GOL E:304 , HOH E:421 , HOH E:485 , HOH E:545 , HOH E:742
BINDING SITE FOR RESIDUE TDR E 301
18
BC9
SOFTWARE
HOH C:501 , MET D:125 , MET E:125 , HOH E:744
BINDING SITE FOR RESIDUE EDO E 302
19
CC1
SOFTWARE
ARG E:178 , HOH E:407 , HOH E:420 , HOH E:581 , HOH E:598 , HOH E:664 , HOH E:745 , LEU F:120
BINDING SITE FOR RESIDUE EDO E 303
20
CC2
SOFTWARE
ILE E:68 , THR E:93 , PHE E:161 , MET E:196 , GLU E:197 , TDR E:301 , HOH E:453 , HOH E:655 , HIS F:7 , HOH F:646
BINDING SITE FOR RESIDUE GOL E 304
21
CC3
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 305
22
CC4
SOFTWARE
THR F:93 , THR F:94 , GLY F:95 , PHE F:161 , GLN F:165 , ARG F:167 , GLU F:195 , MET F:196 , ILE F:219 , ILE F:220 , GOL F:304 , HOH F:406
BINDING SITE FOR RESIDUE TDR F 301
23
CC5
SOFTWARE
GLY F:17 , GLN F:59 , SER F:60 , HOH F:461
BINDING SITE FOR RESIDUE EDO F 302
24
CC6
SOFTWARE
MET A:125 , HOH A:461 , HOH E:493 , MET F:125
BINDING SITE FOR RESIDUE EDO F 303
25
CC7
SOFTWARE
HIS E:7 , PHE F:161 , GLU F:197 , TDR F:301 , HOH F:468 , HOH F:470 , HOH F:557
BINDING SITE FOR RESIDUE GOL F 304
[
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
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 (604 KB)
Header - Asym.Unit
Biol.Unit 1 (598 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
4OGL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
