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3W72
Asym. Unit
Info
Asym.Unit (122 KB)
Biol.Unit 1 (116 KB)
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(1)
Title
:
STRUCTURE OF TRYPANOSOMA CRUZI DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH MII-4-107
Authors
:
D. K. Inaoka, M. Iida, T. Tabuchi, N. Lee, S. Hashimoto, S. Matsuoka, T. K T. Shiba, K. Sakamoto, S. Suzuki, E. O. Balogun, T. Nara, T. Aoki, M. Ino T. Honma, A. Tanaka, S. Harada, K. Kita
Date
:
27 Feb 13 (Deposition) - 05 Mar 14 (Release) - 05 Mar 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.55
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Rossmann Fold, Oxidoreductase, Dihydroorotate/Orotate And Fumarate/Succinate Binding, Cytosol, Oxidoreductase-Oxidoreductase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. K. Inaoka, M. Iida, T. Tabuchi, N. Lee, S. Hashimoto, S. Matsuoka, T. Kuranaga, 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-4-107
To Be Published
[
close entry info
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Hetero Components
(4, 24)
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)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
3a: COBALT HEXAMMINE(III) (NCOa)
4a: 5-[2-(NAPHTHALEN-1-YL)ETHYL]-2,6-D... (W7Ba)
4b: 5-[2-(NAPHTHALEN-1-YL)ETHYL]-2,6-D... (W7Bb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FMN
2
Ligand/Ion
FLAVIN MONONUCLEOTIDE
2
GOL
19
Ligand/Ion
GLYCEROL
3
NCO
1
Ligand/Ion
COBALT HEXAMMINE(III)
4
W7B
2
Ligand/Ion
5-[2-(NAPHTHALEN-1-YL)ETHYL]-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
[
close Hetero Component info
]
Sites
(24, 24)
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)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:43 , ARG A:50 , ASN A:67 , MET A:69 , GLY A:70 , LEU A:71 , SER A:99 , LEU A:101 , ASN A:127 , PRO A:131 , ASN A:194 , SER A:195 , GOL A:404 , FMN A:414 , HOH A:750
BINDING SITE FOR RESIDUE W7B A 401
02
AC2
SOFTWARE
LYS A:214 , PHE A:217 , GOL A:409 , HOH A:525 , HOH A:580 , HOH A:732 , ILE B:171 , ARG B:239
BINDING SITE FOR RESIDUE GOL A 402
03
AC3
SOFTWARE
ILE A:171 , ARG A:239 , GOL A:406 , HOH A:686 , HOH A:688 , LYS B:214 , PHE B:217
BINDING SITE FOR RESIDUE GOL A 403
04
AC4
SOFTWARE
SER A:129 , GLN A:138 , PRO A:166 , ASN A:194 , SER A:195 , GLY A:197 , W7B A:401 , HOH A:530 , HOH A:557 , HOH A:673 , HOH A:750 , HOH A:816
BINDING SITE FOR RESIDUE GOL A 404
05
AC5
SOFTWARE
TYR A:237 , ARG A:238 , PRO A:241 , HOH A:523 , HOH A:806
BINDING SITE FOR RESIDUE GOL A 405
06
AC6
SOFTWARE
ARG A:238 , GOL A:403 , HOH A:666 , HOH A:831 , VAL B:107 , ARG B:111 , GLN B:215 , HOH B:831
BINDING SITE FOR RESIDUE GOL A 406
07
AC7
SOFTWARE
PHE A:61 , VAL A:201 , ASP A:203 , HOH A:551 , HOH A:632 , HOH A:684
BINDING SITE FOR RESIDUE GOL A 407
08
AC8
SOFTWARE
VAL A:10 , TYR A:89 , SER A:90 , LYS A:91 , PRO A:93 , GOL A:410 , HOH A:535 , HOH A:559
BINDING SITE FOR RESIDUE GOL A 408
09
AC9
SOFTWARE
GLN A:215 , GOL A:402 , HOH A:689 , HOH A:691 , ARG B:238
BINDING SITE FOR RESIDUE GOL A 409
10
BC1
SOFTWARE
HIS A:9 , TYR A:89 , LYS A:92 , PRO A:93 , LYS A:120 , GLY A:121 , GOL A:408 , HOH A:543 , HOH A:611 , HOH A:728
BINDING SITE FOR RESIDUE GOL A 410
11
BC2
SOFTWARE
TYR A:58 , MET A:69 , GLN A:275 , HOH A:545 , HOH A:644
BINDING SITE FOR RESIDUE GOL A 411
12
BC3
SOFTWARE
TYR A:141 , PHE A:143 , HIS A:173 , HOH A:550 , HOH A:820 , HIS B:173 , GOL B:407 , GOL B:408
BINDING SITE FOR RESIDUE GOL A 412
13
BC4
SOFTWARE
ASP B:203 , HOH B:733
BINDING SITE FOR RESIDUE GOL A 413
14
BC5
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 , W7B A:401 , HOH A:502 , HOH A:512 , HOH A:526 , HOH A:725
BINDING SITE FOR RESIDUE FMN A 414
15
BC6
SOFTWARE
LYS B:43 , ARG B:50 , ASN B:67 , MET B:69 , GLY B:70 , LEU B:71 , SER B:99 , LEU B:101 , ASN B:127 , SER B:129 , CYS B:130 , PRO B:131 , ASN B:194 , SER B:195 , FMN B:409 , HOH B:577 , HOH B:593
BINDING SITE FOR RESIDUE W7B B 401
16
BC7
SOFTWARE
CYS A:31 , ALA A:34 , SER A:35 , HOH A:774 , CYS B:31 , ALA B:34 , HOH B:506
BINDING SITE FOR RESIDUE GOL B 402
17
BC8
SOFTWARE
ASN A:5 , LEU B:4 , ASN B:5 , GLU B:302 , ARG B:305 , HOH B:596 , HOH B:641 , HOH B:683 , HOH B:834
BINDING SITE FOR RESIDUE GOL B 403
18
BC9
SOFTWARE
PHE B:61 , ASP B:203 , HOH B:564 , HOH B:826 , HOH B:838
BINDING SITE FOR RESIDUE GOL B 404
19
CC1
SOFTWARE
TYR B:58 , HOH B:533 , HOH B:624
BINDING SITE FOR RESIDUE GOL B 405
20
CC2
SOFTWARE
CYS A:1 , LEU A:2 , LYS A:3 , ALA A:12 , ARG B:299 , HOH B:691 , HOH B:800
BINDING SITE FOR RESIDUE GOL B 406
21
CC3
SOFTWARE
HIS A:173 , GOL A:412 , TYR B:141 , PHE B:143 , HIS B:173 , GOL B:408 , HOH B:572 , HOH B:759
BINDING SITE FOR RESIDUE GOL B 407
22
CC4
SOFTWARE
TYR A:141 , TYR A:168 , PHE A:169 , HIS A:173 , GOL A:412 , TYR B:141 , TYR B:168 , PHE B:169 , HIS B:173 , GOL B:407
BINDING SITE FOR RESIDUE GOL B 408
23
CC5
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 , W7B B:401 , HOH B:531 , HOH B:536 , HOH B:546 , HOH B:652
BINDING SITE FOR RESIDUE FMN B 409
24
CC6
SOFTWARE
GLN A:275 , GLU A:276 , GLY A:278 , GLN B:275 , GLU B:276 , GLY B:278 , HOH B:830
BINDING SITE FOR RESIDUE NCO B 410
[
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)
[
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
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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_d3w72a_ (A:)
1b: SCOP_d3w72b_ (B:)
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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
d3w72a_
A:
1b
d3w72b_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
[
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]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
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Asymmetric Unit 1
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