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.
4LAL
Asym. Unit
Info
Asym.Unit (476 KB)
Biol.Unit 1 (238 KB)
Biol.Unit 2 (237 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 CORDYCEPS MILITARIS IDCASE D323A MUTANT IN COMPLEX WITH 5-CARBOXYL-URACIL
Authors
:
S. Xu, W. Li, J. Zhu, J. Ding
Date
:
20 Jun 13 (Deposition) - 02 Oct 13 (Release) - 12 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Pyrimidine Metabolism, Idcase, Decarboxylase, Uracil, Dna Decarboxylation, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Xu, W. Li, J. Zhu, R. Wang, Z. Li, G. L. Xu, J. Ding
Crystal Structures Of Isoorotate Decarboxylases Reveal A Novel Catalytic Mechanism Of 5-Carboxyl-Uracil Decarboxylation And Shed Light On The Search For Dna Decarboxylase.
Cell Res. V. 23 1296 2013
[
close entry info
]
Hetero Components
(3, 19)
Info
All Hetero Components
1a: 2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMI... (5CUa)
1b: 2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMI... (5CUb)
1c: 2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMI... (5CUc)
1d: 2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMI... (5CUd)
2a: HEXAETHYLENE GLYCOL (P6Ga)
2b: HEXAETHYLENE GLYCOL (P6Gb)
2c: HEXAETHYLENE GLYCOL (P6Gc)
2d: HEXAETHYLENE GLYCOL (P6Gd)
2e: HEXAETHYLENE GLYCOL (P6Ge)
2f: HEXAETHYLENE GLYCOL (P6Gf)
2g: HEXAETHYLENE GLYCOL (P6Gg)
2h: HEXAETHYLENE GLYCOL (P6Gh)
2i: HEXAETHYLENE GLYCOL (P6Gi)
2j: HEXAETHYLENE GLYCOL (P6Gj)
2k: HEXAETHYLENE GLYCOL (P6Gk)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
5CU
4
Ligand/Ion
2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDINE-5-CARBOXYLICACID
2
P6G
11
Ligand/Ion
HEXAETHYLENE GLYCOL
3
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:12 , HIS A:14 , HIS A:195 , 5CU A:402
BINDING SITE FOR RESIDUE ZN A 401
02
AC2
SOFTWARE
HIS A:12 , HIS A:14 , ARG A:68 , ASN A:98 , HIS A:195 , LEU A:218 , PHE A:222 , HIS A:251 , PHE A:326 , PHE A:327 , ZN A:401 , ARG B:262 , HOH B:506
BINDING SITE FOR RESIDUE 5CU A 402
03
AC3
SOFTWARE
LYS A:291 , ALA A:311
BINDING SITE FOR RESIDUE P6G A 403
04
AC4
SOFTWARE
ARG A:152 , ARG C:152
BINDING SITE FOR RESIDUE P6G A 404
05
AC5
SOFTWARE
GLN A:38 , PRO A:61 , ASP A:144 , LYS A:147 , PRO A:180
BINDING SITE FOR RESIDUE P6G A 405
06
AC6
SOFTWARE
ALA A:186 , LYS A:189 , LEU A:190 , ASN A:244 , GLN A:246 , HOH A:630 , GLY C:355 , SER C:357
BINDING SITE FOR RESIDUE P6G A 406
07
AC7
SOFTWARE
HIS B:12 , HIS B:14 , HIS B:195 , 5CU B:402
BINDING SITE FOR RESIDUE ZN B 401
08
AC8
SOFTWARE
ARG A:262 , HOH A:519 , HIS B:12 , HIS B:14 , ARG B:68 , ASN B:98 , HIS B:195 , LEU B:218 , PHE B:222 , HIS B:251 , PHE B:326 , PHE B:327 , ZN B:401
BINDING SITE FOR RESIDUE 5CU B 402
09
AC9
SOFTWARE
ARG A:208 , TYR B:234 , MET B:235 , ALA B:236 , GLY B:237 , ASP B:240 , LYS B:278 , HOH B:559
BINDING SITE FOR RESIDUE P6G B 403
10
BC1
SOFTWARE
HIS C:12 , HIS C:14 , HIS C:195 , 5CU C:402
BINDING SITE FOR RESIDUE ZN C 401
11
BC2
SOFTWARE
HIS C:12 , HIS C:14 , ARG C:68 , ASN C:98 , HIS C:195 , LEU C:218 , PHE C:222 , HIS C:251 , PHE C:326 , PHE C:327 , ZN C:401 , ARG D:262 , HOH D:503
BINDING SITE FOR RESIDUE 5CU C 402
12
BC3
SOFTWARE
TRP C:287 , LYS C:291 , ALA C:311 , TYR D:301 , SER D:302 , GLU D:303 , LEU D:343 , LYS D:350
BINDING SITE FOR RESIDUE P6G C 403
13
BC4
SOFTWARE
LYS C:189 , GLN C:246
BINDING SITE FOR RESIDUE P6G C 404
14
BC5
SOFTWARE
TYR C:234 , MET C:235 , GLY C:237 , ASP C:240 , LYS C:278
BINDING SITE FOR RESIDUE P6G C 405
15
BC6
SOFTWARE
PRO C:37 , GLN C:38 , LYS C:147 , PRO C:180 , GLU C:183
BINDING SITE FOR RESIDUE P6G C 406
16
BC7
SOFTWARE
HIS D:12 , HIS D:14 , HIS D:195 , 5CU D:402
BINDING SITE FOR RESIDUE ZN D 401
17
BC8
SOFTWARE
ARG C:262 , HIS D:12 , HIS D:14 , ARG D:68 , ASN D:98 , HIS D:195 , LEU D:218 , PHE D:222 , HIS D:251 , ALA D:323 , PHE D:326 , PHE D:327 , ZN D:401 , HOH D:508
BINDING SITE FOR RESIDUE 5CU D 402
18
BC9
SOFTWARE
TRP D:287 , LYS D:291
BINDING SITE FOR RESIDUE P6G D 403
19
CC1
SOFTWARE
GLU C:211 , ASP C:282 , TYR D:234 , MET D:235 , ASP D:240 , LYS D:278
BINDING SITE FOR RESIDUE P6G D 404
[
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
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 (476 KB)
Header - Asym.Unit
Biol.Unit 1 (238 KB)
Header - Biol.Unit 1
Biol.Unit 2 (237 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
4LAL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
