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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2QCM
Asym. Unit
Info
Asym.Unit (55 KB)
Biol.Unit 1 (99 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 OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE DOMAIN (ASP312ASN MUTANT) OF HUMAN UMP SYNTHASE BOUND TO 6-HYDROXYMETHYL-UMP
Authors
:
J. Wittmann, M. Rudolph
Date
:
19 Jun 07 (Deposition) - 06 Nov 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.67
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Ump Synthase, Decarboxylase, Catalytic Proficiency, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. G. Wittmann, D. Heinrich, K. Gasow, A. Frey, U. Diederichsen, M. G. Rudolph
Structures Of The Human Orotidine-5'-Monophosphate Decarboxylase Support A Covalent Mechanism And Provide A Framework For Drug Design.
Structure V. 16 82 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: S-MERCAPTOCYSTEINE (CSSa)
2a: 6-(HYDROXYMETHYL)URIDINE 5'-(DIHYD... (JW5a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSS
1
Mod. Amino Acid
S-MERCAPTOCYSTEINE
2
JW5
1
Ligand/Ion
6-(HYDROXYMETHYL)URIDINE 5'-(DIHYDROGEN PHOSPHATE)
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:257 , ASP A:259 , LYS A:281 , HIS A:283 , ASN A:312 , ASP A:317 , ILE A:318 , THR A:321 , ASN A:341 , MET A:371 , SER A:372 , ILE A:401 , PRO A:417 , GLN A:430 , TYR A:432 , GLY A:450 , ARG A:451 , HOH A:488 , HOH A:494 , HOH A:530
BINDING SITE FOR RESIDUE JW5 A 482
[
close Site info
]
SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_006810 (G429R, chain A, )
2: VAR_020615 (I446V, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_006810
G
429
R
UMPS_HUMAN
Disease (ORAC1)
---
A
G
429
R
2
UniProt
VAR_020615
I
446
V
UMPS_HUMAN
Polymorphism
3772809
A
I
446
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: OMPDECASE (A:309-322)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
OMPDECASE
PS00156
Orotidine 5'-phosphate decarboxylase active site.
UMPS_HUMAN
309-322
1
A:309-322
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.5a (A:223-328)
Exon 1.7 (A:328-386)
Exon 1.8a (A:387-425)
Exon 1.9d (A:425-479)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3/1.5a
2: Boundary 1.5a/1.7
3: Boundary 1.7/1.8a
4: Boundary 1.8a/1.9d
5: Boundary 1.9d/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000232607
1a
ENSE00000823837
chr3:
124449213-124449474
262
UMPS_HUMAN
1-52
52
0
-
-
1.3
ENST00000232607
3
ENSE00000776933
chr3:
124453940-124454093
154
UMPS_HUMAN
53-104
52
0
-
-
1.5a
ENST00000232607
5a
ENSE00000776934
chr3:
124456415-124457086
672
UMPS_HUMAN
104-328
225
1
A:223-328
106
1.7
ENST00000232607
7
ENSE00000823838
chr3:
124458871-124459046
176
UMPS_HUMAN
328-386
59
1
A:328-386
59
1.8a
ENST00000232607
8a
ENSE00000823839
chr3:
124460999-124461113
115
UMPS_HUMAN
387-425
39
1
A:387-425
39
1.9d
ENST00000232607
9d
ENSE00001382696
chr3:
124462762-124464040
1279
UMPS_HUMAN
425-480
56
1
A:425-479
55
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2qcmA00 (A:223-479)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Human (Homo sapiens)
(78)
1a
2qcmA00
A:223-479
[
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
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 (55 KB)
Header - Asym.Unit
Biol.Unit 1 (99 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
2QCM
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
