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.
1D3G
Asym. Unit
Info
Asym.Unit (132 KB)
Biol.Unit 1 (128 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN DIHYDROOROTATE DEHYDROGENASE COMPLEXED WITH BREQUINAR ANALOG
Authors
:
S. Liu, E. A. Neidhardt, T. H. Grossman, T. Ocain, J. Clardy
Date
:
29 Sep 99 (Deposition) - 13 Sep 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Protein-Antiproliferative Agent Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Liu, E. A. Neidhardt, T. H. Grossman, T. Ocain, J. Clardy
Structures Of Human Dihydroorotate Dehydrogenase In Complex With Antiproliferative Agents.
Structure Fold. Des. V. 8 25 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(6, 6)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: 2-BIPHENYL-4-YL-6-FLUORO-3-METHYL-... (BREa)
3a: DECYLAMINE-N,N-DIMETHYL-N-OXIDE (DDQa)
4a: FLAVIN MONONUCLEOTIDE (FMNa)
5a: OROTIC ACID (OROa)
6a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
BRE
1
Ligand/Ion
2-BIPHENYL-4-YL-6-FLUORO-3-METHYL-QUINOLINE-4-CARBOXYLIC ACID
3
DDQ
1
Ligand/Ion
DECYLAMINE-N,N-DIMETHYL-N-OXIDE
4
FMN
1
Ligand/Ion
FLAVIN MONONUCLEOTIDE
5
ORO
1
Ligand/Ion
OROTIC ACID
6
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
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:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:245 , VAL A:247 , HIS A:248 , HOH A:649
BINDING SITE FOR RESIDUE SO4 A 400
2
AC2
SOFTWARE
LYS A:307 , PRO A:308 , ASP A:311 , THR A:314 , GLN A:315 , ARG A:318 , HOH A:418
BINDING SITE FOR RESIDUE ACT A 401
3
AC3
SOFTWARE
LEU A:46 , GLN A:47 , PRO A:52 , ALA A:55 , HIS A:56 , ALA A:59 , LEU A:67 , LEU A:68 , VAL A:134 , ARG A:136 , TYR A:356 , THR A:360 , HOH A:444 , DDQ A:700
BINDING SITE FOR RESIDUE BRE A 397
4
AC4
SOFTWARE
ALA A:95 , ALA A:96 , GLY A:97 , LYS A:100 , GLY A:119 , SER A:120 , ASN A:145 , ASN A:181 , ASN A:212 , LYS A:255 , THR A:283 , ASN A:284 , THR A:285 , SER A:305 , GLY A:306 , LEU A:309 , VAL A:333 , GLY A:334 , GLY A:335 , LEU A:355 , TYR A:356 , THR A:357 , ORO A:399 , HOH A:403 , HOH A:405
BINDING SITE FOR RESIDUE FMN A 398
5
AC5
SOFTWARE
LYS A:100 , ASN A:145 , TYR A:147 , GLY A:148 , PHE A:149 , ASN A:212 , SER A:215 , ASN A:217 , ASN A:284 , THR A:285 , FMN A:398
BINDING SITE FOR RESIDUE ORO A 399
6
AC6
SOFTWARE
MET A:30 , ALA A:31 , TYR A:38 , LEU A:58 , PHE A:62 , LEU A:68 , BRE A:397
BINDING SITE FOR RESIDUE DDQ A 700
[
close Site info
]
SAPs(SNPs)/Variants
(9, 9)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_062413 (R136C, chain A, )
2: VAR_062414 (G153R, chain A, )
3: VAR_062415 (R200C, chain A, )
4: VAR_062416 (G203A, chain A, )
5: VAR_062417 (G203D, chain A, )
6: VAR_062418 (R245W, chain A, )
7: VAR_062419 (T285I, chain A, )
8: VAR_062420 (R347W, chain A, )
9: VAR_062421 (D393G, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_062413
R
135
C
PYRD_HUMAN
Disease (POADS)
---
A
R
136
C
2
UniProt
VAR_062414
G
152
R
PYRD_HUMAN
Disease (POADS)
---
A
G
153
R
3
UniProt
VAR_062415
R
199
C
PYRD_HUMAN
Disease (POADS)
---
A
R
200
C
4
UniProt
VAR_062416
G
202
A
PYRD_HUMAN
Disease (POADS)
---
A
G
203
A
5
UniProt
VAR_062417
G
202
D
PYRD_HUMAN
Disease (POADS)
---
A
G
203
D
6
UniProt
VAR_062418
R
244
W
PYRD_HUMAN
Disease (POADS)
---
A
R
245
W
7
UniProt
VAR_062419
T
284
I
PYRD_HUMAN
Disease (POADS)
---
A
T
285
I
8
UniProt
VAR_062420
R
346
W
PYRD_HUMAN
Disease (POADS)
---
A
R
347
W
9
UniProt
VAR_062421
D
392
G
PYRD_HUMAN
Disease (POADS)
---
A
D
393
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: DHODEHASE_1 (A:114-133)
2: DHODEHASE_2 (A:330-350)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DHODEHASE_1
PS00911
Dihydroorotate dehydrogenase signature 1.
PYRD_HUMAN
113-132
1
A:114-133
2
DHODEHASE_2
PS00912
Dihydroorotate dehydrogenase signature 2.
PYRD_HUMAN
329-349
1
A:330-350
[
close PROSITE info
]
Exons
(8, 8)
Info
All Exons
Exon 1.2 (A:30-79 (gaps))
Exon 1.3 (A:80-146)
Exon 1.4 (A:146-174)
Exon 1.5 (A:174-236 (gaps))
Exon 1.6 (A:237-274)
Exon 1.7 (A:275-326)
Exon 1.8 (A:326-379)
Exon 1.9 (A:379-396)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7
7: Boundary 1.7/1.8
8: Boundary 1.8/1.9
9: Boundary 1.9/-
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
1.1
ENST00000219240
1
ENSE00001420633
chr16:
72042643-72042684
42
PYRD_HUMAN
1-7
7
0
-
-
1.2
ENST00000219240
2
ENSE00000799143
chr16:
72045949-72046161
213
PYRD_HUMAN
8-78
71
1
A:30-79 (gaps)
50
1.3
ENST00000219240
3
ENSE00000692663
chr16:
72048372-72048571
200
PYRD_HUMAN
79-145
67
1
A:80-146
67
1.4
ENST00000219240
4
ENSE00000692662
chr16:
72050923-72051005
83
PYRD_HUMAN
145-173
29
1
A:146-174
29
1.5
ENST00000219240
5
ENSE00000692661
chr16:
72055023-72055210
188
PYRD_HUMAN
173-235
63
1
A:174-236 (gaps)
63
1.6
ENST00000219240
6
ENSE00000692660
chr16:
72056261-72056374
114
PYRD_HUMAN
236-273
38
1
A:237-274
38
1.7
ENST00000219240
7
ENSE00001718063
chr16:
72057064-72057217
154
PYRD_HUMAN
274-325
52
1
A:275-326
52
1.8
ENST00000219240
8
ENSE00001662402
chr16:
72057373-72057532
160
PYRD_HUMAN
325-378
54
1
A:326-379
54
1.9
ENST00000219240
9
ENSE00001737850
chr16:
72058044-72058954
911
PYRD_HUMAN
378-395
18
1
A:379-396
18
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1d3ga_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
FMN-linked oxidoreductases
(290)
Family
:
FMN-linked oxidoreductases
(242)
Protein domain
:
Dihydroorotate dehydrogenase
(90)
Human (Homo sapiens) [TaxId: 9606]
(24)
1a
d1d3ga_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1d3gA00 (A:30-396)
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
1d3gA00
A:30-396
[
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 (132 KB)
Header - Asym.Unit
Biol.Unit 1 (128 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
1D3G
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
