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.
3W1X
Asym. Unit
Info
Asym.Unit (122 KB)
Biol.Unit 1 (116 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF TRYPANOSOMA CRUZI DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH MII-3-121
Authors
:
D. K. Inaoka, M. Iida, T. Tabuchi, N. Lee, S. Matsuoka, T. Shiba, K. Sakam S. Suzuki, E. O. Balogun, T. Nara, T. Aoki, M. Inoue, T. Honma, A. Tanaka S. Harada, K. Kita
Date
:
22 Nov 12 (Deposition) - 27 Nov 13 (Release) - 27 Nov 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.45
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Rossmann Fold, Oxidoreductase, Dihydroorotate/Orotate Binding, Cytosol, Oxidoreductase-Oxidoreductase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. K. Inaoka, M. Iida, T. Tabuchi, N. Lee, S. Matsuoka, T. Shiba, K. Sakamoto, S. Suzuki, E. O. Balogun, T. Nara, T. Aoki, M. Inoue, T. Honma, A. Tanaka, S. Harada, K. Kita
Structure Of Trypanosoma Cruzi Dihydroorotate Dehydrogenase In Complex With Mii-3-121.
To Be Published
[
close entry info
]
Hetero Components
(4, 21)
Info
All Hetero Components
1a: FLAVIN MONONUCLEOTIDE (FMNa)
1b: FLAVIN MONONUCLEOTIDE (FMNb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
3a: COBALT HEXAMMINE(III) (NCOa)
4a: 5-{2-[4-(CYANOMETHYL)PHENYL]ETHYL}... (XROa)
4b: 5-{2-[4-(CYANOMETHYL)PHENYL]ETHYL}... (XROb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FMN
2
Ligand/Ion
FLAVIN MONONUCLEOTIDE
2
GOL
16
Ligand/Ion
GLYCEROL
3
NCO
1
Ligand/Ion
COBALT HEXAMMINE(III)
4
XRO
2
Ligand/Ion
5-{2-[4-(CYANOMETHYL)PHENYL]ETHYL}-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:43 , ASN A:53 , ASN A:67 , SER A:68 , MET A:69 , GLY A:70 , LEU A:71 , ASN A:127 , SER A:129 , PRO A:131 , ASN A:194 , SER A:195 , GOL A:405 , FMN A:411 , HOH A:511 , HOH A:820
BINDING SITE FOR RESIDUE XRO A 401
02
AC2
SOFTWARE
CYS A:31 , ALA A:34 , HOH A:532 , CYS B:31 , ALA B:34 , SER B:35 , PRO B:279 , HOH B:683
BINDING SITE FOR RESIDUE GOL A 402
03
AC3
SOFTWARE
ILE A:171 , ARG A:239 , GOL A:410 , HOH A:814 , HOH A:856 , LYS B:214 , PHE B:217 , HOH B:602
BINDING SITE FOR RESIDUE GOL A 403
04
AC4
SOFTWARE
TYR A:237 , PRO A:241 , HOH A:573 , HOH A:693
BINDING SITE FOR RESIDUE GOL A 404
05
AC5
SOFTWARE
SER A:129 , GLN A:138 , PRO A:166 , ASN A:194 , SER A:195 , XRO A:401 , HOH A:522 , HOH A:530 , HOH A:562 , HOH A:820
BINDING SITE FOR RESIDUE GOL A 405
06
AC6
SOFTWARE
LEU A:4 , ASN A:5 , GLU A:302 , HOH A:790 , HOH A:886 , LYS B:3 , ASN B:5 , VAL B:10 , HOH B:832
BINDING SITE FOR RESIDUE GOL A 406
07
AC7
SOFTWARE
PHE A:61 , ILE A:202 , ASP A:203 , HOH A:582 , HOH A:686 , HOH A:703
BINDING SITE FOR RESIDUE GOL A 407
08
AC8
SOFTWARE
TYR A:58 , HOH A:540 , HOH A:633 , HOH A:659
BINDING SITE FOR RESIDUE GOL A 408
09
AC9
SOFTWARE
HOH A:803 , CYS B:1 , LEU B:2 , LYS B:3 , ALA B:12 , HOH B:579 , HOH B:779
BINDING SITE FOR RESIDUE GOL A 409
10
BC1
SOFTWARE
ARG A:238 , GOL A:403 , HOH A:577 , HOH A:854 , GLN B:215 , HOH B:672
BINDING SITE FOR RESIDUE GOL A 410
11
BC2
SOFTWARE
ALA A:18 , ALA A:19 , GLY A:20 , LYS A:43 , SER A:44 , ASN A:67 , ASN A:127 , LYS A:164 , VAL A:193 , ASN A:194 , GLY A:221 , GLY A:222 , ILE A:225 , CYS A:248 , GLY A:249 , GLY A:250 , GLY A:271 , THR A:272 , XRO A:401 , HOH A:508 , HOH A:517 , HOH A:528 , HOH A:815
BINDING SITE FOR RESIDUE FMN A 411
12
BC3
SOFTWARE
GLN A:275 , GLU A:276 , GLY A:278 , HOH A:669 , HOH A:780 , HOH A:789 , HOH A:818 , GLN B:275 , GLU B:276 , GLY B:278
BINDING SITE FOR RESIDUE NCO A 412
13
BC4
SOFTWARE
LYS B:43 , ASN B:53 , ASN B:67 , SER B:68 , MET B:69 , GLY B:70 , LEU B:71 , ASN B:127 , SER B:129 , PRO B:131 , ASN B:194 , SER B:195 , GOL B:403 , FMN B:409 , HOH B:826
BINDING SITE FOR RESIDUE XRO B 401
14
BC5
SOFTWARE
LYS A:214 , PHE A:217 , HOH A:542 , ILE B:171 , ARG B:239 , HOH B:558
BINDING SITE FOR RESIDUE GOL B 402
15
BC6
SOFTWARE
SER B:129 , PRO B:166 , ASN B:194 , SER B:195 , GLY B:197 , GLY B:219 , XRO B:401 , HOH B:515 , HOH B:826 , HOH B:827
BINDING SITE FOR RESIDUE GOL B 403
16
BC7
SOFTWARE
TYR B:237 , ARG B:238 , PRO B:241 , HOH B:539 , HOH B:744
BINDING SITE FOR RESIDUE GOL B 404
17
BC8
SOFTWARE
SER A:47 , ASN B:182 , ARG B:239 , PRO B:241 , HOH B:592 , HOH B:693 , HOH B:745 , HOH B:823
BINDING SITE FOR RESIDUE GOL B 405
18
BC9
SOFTWARE
PHE B:61 , ASP B:203 , HOH B:621 , HOH B:729 , HOH B:732
BINDING SITE FOR RESIDUE GOL B 406
19
CC1
SOFTWARE
ASP B:203 , SER B:206 , SER B:208 , VAL B:209 , HOH B:646 , HOH B:729
BINDING SITE FOR RESIDUE GOL B 407
20
CC2
SOFTWARE
VAL B:10 , TYR B:89 , SER B:90 , LYS B:91 , PRO B:93 , HOH B:513 , HOH B:793 , HOH B:807 , HOH B:879
BINDING SITE FOR RESIDUE GOL B 408
21
CC3
SOFTWARE
ALA B:18 , ALA B:19 , GLY B:20 , LYS B:43 , SER B:44 , ASN B:67 , ASN B:127 , LYS B:164 , VAL B:193 , ASN B:194 , GLY B:221 , GLY B:222 , ILE B:225 , CYS B:248 , GLY B:249 , GLY B:250 , GLY B:271 , THR B:272 , XRO B:401 , HOH B:506 , HOH B:518 , HOH B:523 , HOH B:824
BINDING SITE FOR RESIDUE FMN B 409
[
close Site info
]
SAPs(SNPs)/Variants
(8, 16)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_PYRD_TRYCC_001 (M0T, chain A/B, )
2: VAR_PYRD_TRYCC_002 (C1R, chain A/B, )
3: VAR_PYRD_TRYCC_003 (F61V, chain A/B, )
4: VAR_PYRD_TRYCC_004 (S84I, chain A/B, )
5: VAR_PYRD_TRYCC_005 (L96V, chain A/B, )
6: VAR_PYRD_TRYCC_006 (L220I, chain A/B, )
7: VAR_PYRD_TRYCC_007 (T283R, chain A/B, )
8: VAR_PYRD_TRYCC_008 (R299K, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_PYRD_TRYCC_001
*
M
2
T
PYRD_TRYCC
---
---
A/B
M
0
T
2
UniProt
VAR_PYRD_TRYCC_002
*
C
3
R
PYRD_TRYCC
---
---
A/B
C
1
R
3
UniProt
VAR_PYRD_TRYCC_003
*
F
63
V
PYRD_TRYCC
---
---
A/B
F
61
V
4
UniProt
VAR_PYRD_TRYCC_004
*
S
86
I
PYRD_TRYCC
---
---
A/B
S
84
I
5
UniProt
VAR_PYRD_TRYCC_005
*
L
98
V
PYRD_TRYCC
---
---
A/B
L
96
V
6
UniProt
VAR_PYRD_TRYCC_006
*
L
222
I
PYRD_TRYCC
---
---
A/B
L
220
I
7
UniProt
VAR_PYRD_TRYCC_007
*
T
285
R
PYRD_TRYCC
---
---
A/B
T
283
R
8
UniProt
VAR_PYRD_TRYCC_008
*
R
301
K
PYRD_TRYCC
---
---
A/B
R
299
K
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3w1xa_ (A:)
1b: SCOP_d3w1xb_ (B:)
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)
Trypanosoma cruzi [TaxId: 353153]
(49)
1a
d3w1xa_
A:
1b
d3w1xb_
B:
[
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
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 (122 KB)
Header - Asym.Unit
Biol.Unit 1 (116 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
3W1X
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
