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3G3D
Asym. Unit
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Asym.Unit (100 KB)
Biol.Unit 1 (94 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE COVALENTLY MODIFIED BY 5-FLUORO-6-AZIDO-UMP
Authors
:
Y. Liu, H. L. Tang, A. Bello, E. Poduch, L. Kotra, E. Pai
Date
:
02 Feb 09 (Deposition) - 03 Mar 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Ump Synthase, C-Terminal Domain, Orotidine 5'-Monophosphate Decarboxylase, Human, 5-Fluoro-6-Azido-Ump, Decarboxylase, Disease Mutation, Glycosyltransferase, Lyase, Multifunctional Enzyme, Phosphoprotein, Pyrimidine Biosynthesis, Transferase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
A. M. Bello, D. Konforte, E. Poduch, C. Furlonger, L. Wei, Y. Liu, M. Lewis, E. F. Pai, C. J. Paige, L. P. Kotra
Structure-Activity Relationships Of Orotidine-5'-Monophosphate Decarboxylase Inhibitors As Anticancer Agents.
J. Med. Chem. V. 52 1648 2009
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: 5-FLUORO-URIDINE-5'-MONOPHOSPHATE (5FUa)
1b: 5-FLUORO-URIDINE-5'-MONOPHOSPHATE (5FUb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
3a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
5FU
2
Ligand/Ion
5-FLUORO-URIDINE-5'-MONOPHOSPHATE
2
GOL
3
Ligand/Ion
GLYCEROL
3
SO4
1
Ligand/Ion
SULFATE ION
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:68 , ASP A:70 , LYS A:92 , HIS A:94 , ASP A:123 , LYS A:125 , MET A:182 , SER A:183 , PRO A:228 , GLN A:241 , TYR A:243 , GLY A:261 , ARG A:262 , HOH A:295 , HOH A:297 , HOH A:298 , HOH A:330 , ASP B:128 , ILE B:129 , THR B:132
BINDING SITE FOR RESIDUE 5FU A3000
2
AC2
SOFTWARE
ASP A:128 , ILE A:129 , THR A:132 , SER B:68 , ASP B:70 , LYS B:92 , HIS B:94 , ASP B:123 , LYS B:125 , MET B:182 , SER B:183 , PRO B:228 , GLN B:241 , TYR B:243 , GLY B:261 , ARG B:262 , HOH B:300 , HOH B:338 , HOH B:345
BINDING SITE FOR RESIDUE 5FU B3000
3
AC3
SOFTWARE
LYS A:53 , ALA A:113 , LYS A:114 , PHE A:118 , LEU A:119 , ASP A:149 , HOH A:390
BINDING SITE FOR RESIDUE GOL A1000
4
AC4
SOFTWARE
LEU B:73 , ARG B:75
BINDING SITE FOR RESIDUE GOL B1001
5
AC5
SOFTWARE
ASP B:269 , GLU B:272 , MET B:276 , HOH B:348 , HOH B:425
BINDING SITE FOR RESIDUE GOL B1002
6
AC6
SOFTWARE
GLY B:39 , ALA B:40 , GLU B:43 , HOH B:359
BINDING SITE FOR RESIDUE SO4 B2000
[
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_006810 (G240R, chain A/B, )
2: VAR_020615 (I257V, chain A/B, )
View:
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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/B
G
240
R
2
UniProt
VAR_020615
I
446
V
UMPS_HUMAN
Polymorphism
3772809
A/B
I
257
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: OMPDECASE (A:120-133,B:120-133)
;
View:
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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
2
A:120-133
B:120-133
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Exons
(4, 8)
Info
All Exons
Exon 1.5a (A:35-139 | B:32-139)
Exon 1.7 (A:139-197 | B:139-197)
Exon 1.8a (A:198-236 | B:198-236)
Exon 1.9d (A:236-290 | B:236-290)
View:
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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:
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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
2
A:35-139
B:32-139
105
108
1.7
ENST00000232607
7
ENSE00000823838
chr3:
124458871-124459046
176
UMPS_HUMAN
328-386
59
2
A:139-197
B:139-197
59
59
1.8a
ENST00000232607
8a
ENSE00000823839
chr3:
124460999-124461113
115
UMPS_HUMAN
387-425
39
2
A:198-236
B:198-236
39
39
1.9d
ENST00000232607
9d
ENSE00001382696
chr3:
124462762-124464040
1279
UMPS_HUMAN
425-480
56
2
A:236-290
B:236-290
55
55
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SCOP Domains
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3g3dA00 (A:35-290)
1b: CATH_3g3dB00 (B:32-290)
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Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Human (Homo sapiens)
(78)
1a
3g3dA00
A:35-290
1b
3g3dB00
B:32-290
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Pfam Domains
(0, 0)
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