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3W7R
Asym. Unit
Info
Asym.Unit (83 KB)
Biol.Unit 1 (75 KB)
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(1)
Title
:
STRUCTURE OF HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH MII-4-097
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
:
06 Mar 13 (Deposition) - 12 Mar 14 (Release) - 12 Mar 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.68
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Rossmann Fold, Oxidoreductase, Dihydroorotate/Orotate And Ubiquinone/Ubiquinol, Mitochondrial Inner Membrane, 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 Human Dihydroorotate Dehydrogenase In Complex With Mii-4-097
To Be Published
[
close entry info
]
Hetero Components
(8, 43)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
2a: CHLORIDE ION (CLa)
3a: DECYLAMINE-N,N-DIMETHYL-N-OXIDE (DDQa)
3b: DECYLAMINE-N,N-DIMETHYL-N-OXIDE (DDQb)
3c: DECYLAMINE-N,N-DIMETHYL-N-OXIDE (DDQc)
3d: DECYLAMINE-N,N-DIMETHYL-N-OXIDE (DDQd)
3e: DECYLAMINE-N,N-DIMETHYL-N-OXIDE (DDQe)
3f: DECYLAMINE-N,N-DIMETHYL-N-OXIDE (DDQf)
4a: FLAVIN MONONUCLEOTIDE (FMNa)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
5d: GLYCEROL (GOLd)
5e: GLYCEROL (GOLe)
5f: GLYCEROL (GOLf)
5g: GLYCEROL (GOLg)
5h: GLYCEROL (GOLh)
5i: GLYCEROL (GOLi)
5j: GLYCEROL (GOLj)
5k: GLYCEROL (GOLk)
5l: GLYCEROL (GOLl)
5m: GLYCEROL (GOLm)
5n: GLYCEROL (GOLn)
5o: GLYCEROL (GOLo)
5p: GLYCEROL (GOLp)
5q: GLYCEROL (GOLq)
5r: GLYCEROL (GOLr)
5s: GLYCEROL (GOLs)
5t: GLYCEROL (GOLt)
5u: GLYCEROL (GOLu)
5v: GLYCEROL (GOLv)
6a: OROTIC ACID (OROa)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
7c: SULFATE ION (SO4c)
7d: SULFATE ION (SO4d)
8a: 2,6-DIOXO-5-[2-(4-PHENYLPHENYL)ETH... (W7Aa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
7
Ligand/Ion
ACETATE ION
2
CL
1
Ligand/Ion
CHLORIDE ION
3
DDQ
6
Ligand/Ion
DECYLAMINE-N,N-DIMETHYL-N-OXIDE
4
FMN
1
Ligand/Ion
FLAVIN MONONUCLEOTIDE
5
GOL
22
Ligand/Ion
GLYCEROL
6
ORO
1
Ligand/Ion
OROTIC ACID
7
SO4
4
Ligand/Ion
SULFATE ION
8
W7A
1
Ligand/Ion
2,6-DIOXO-5-[2-(4-PHENYLPHENYL)ETHYL]-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
[
close Hetero Component info
]
Sites
(43, 43)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:165 , HIS A:248 , ARG A:298 , SER A:299
BINDING SITE FOR RESIDUE CL A 401
02
AC2
SOFTWARE
HIS A:41 , THR A:45
BINDING SITE FOR RESIDUE DDQ A 402
03
AC3
SOFTWARE
DDQ A:404
BINDING SITE FOR RESIDUE DDQ A 403
04
AC4
SOFTWARE
GLN A:47 , GLY A:48 , LEU A:49 , DDQ A:403 , HOH A:659
BINDING SITE FOR RESIDUE DDQ A 404
05
AC5
SOFTWARE
PHE A:62
BINDING SITE FOR RESIDUE DDQ A 405
06
AC6
SOFTWARE
GLY A:33 , PHE A:37 , GLU A:40 , HIS A:41
BINDING SITE FOR RESIDUE DDQ A 406
07
AC7
SOFTWARE
LEU A:68 , W7A A:408 , HOH A:772
BINDING SITE FOR RESIDUE DDQ A 407
08
AC8
SOFTWARE
MET A:43 , GLN A:47 , PRO A:52 , ALA A:55 , HIS A:56 , ALA A:59 , LEU A:67 , LEU A:68 , PHE A:98 , VAL A:134 , ARG A:136 , TYR A:356 , THR A:360 , PRO A:364 , DDQ A:407 , FMN A:409 , HOH A:691
BINDING SITE FOR RESIDUE W7A A 408
09
AC9
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 , W7A A:408 , ORO A:432 , HOH A:503 , HOH A:529
BINDING SITE FOR RESIDUE FMN A 409
10
BC1
SOFTWARE
LYS A:307 , THR A:314 , GLN A:315 , ARG A:318 , GLU A:344 , HOH A:524 , HOH A:557 , HOH A:779
BINDING SITE FOR RESIDUE GOL A 410
11
BC2
SOFTWARE
HIS A:159 , ALA A:322 , GLN A:325 , HIS A:394 , HOH A:537 , HOH A:574 , HOH A:617
BINDING SITE FOR RESIDUE GOL A 411
12
BC3
SOFTWARE
SER A:223 , ASP A:264 , HOH A:674
BINDING SITE FOR RESIDUE GOL A 412
13
BC4
SOFTWARE
ARG A:57 , HIS A:101 , ASN A:150 , HIS A:152 , GOL A:416 , HOH A:541 , HOH A:645 , HOH A:731
BINDING SITE FOR RESIDUE GOL A 413
14
BC5
SOFTWARE
ARG A:61 , SER A:64 , GLU A:103 , ACT A:439 , HOH A:668 , HOH A:762
BINDING SITE FOR RESIDUE GOL A 414
15
BC6
SOFTWARE
ALA A:219 , GLY A:220 , ARG A:222 , HOH A:791
BINDING SITE FOR RESIDUE GOL A 415
16
BC7
SOFTWARE
GLN A:126 , GLU A:127 , SER A:151 , HIS A:152 , GOL A:413 , HOH A:535 , HOH A:701
BINDING SITE FOR RESIDUE GOL A 416
17
BC8
SOFTWARE
GLU A:139 , SER A:155 , GLU A:158 , HIS A:159 , ARG A:162 , GLN A:294 , ALA A:296 , GOL A:424 , HOH A:754
BINDING SITE FOR RESIDUE GOL A 417
18
BC9
SOFTWARE
ARG A:136 , PRO A:138 , HOH A:575 , HOH A:732 , HOH A:776
BINDING SITE FOR RESIDUE GOL A 418
19
CC1
SOFTWARE
ARG A:241 , ARG A:249 , PRO A:250 , ALA A:251 , ASP A:278 , GOL A:420 , HOH A:609 , HOH A:738 , HOH A:796 , HOH A:797
BINDING SITE FOR RESIDUE GOL A 419
20
CC2
SOFTWARE
HIS A:86 , ASP A:207 , ARG A:246 , VAL A:247 , ARG A:249 , GOL A:419 , ACT A:438 , HOH A:783
BINDING SITE FOR RESIDUE GOL A 420
21
CC3
SOFTWARE
HIS A:86 , LYS A:87 , THR A:172 , GLU A:173 , HOH A:804
BINDING SITE FOR RESIDUE GOL A 421
22
CC4
SOFTWARE
PRO A:52 , PRO A:132 , VAL A:134 , PHE A:135 , ARG A:200 , HOH A:562 , HOH A:659
BINDING SITE FOR RESIDUE GOL A 422
23
CC5
SOFTWARE
MET A:30 , THR A:32 , GLY A:33 , ARG A:72 , HOH A:771
BINDING SITE FOR RESIDUE GOL A 423
24
CC6
SOFTWARE
LYS A:124 , SER A:155 , GLU A:197 , GOL A:417 , ACT A:437 , HOH A:776
BINDING SITE FOR RESIDUE GOL A 424
25
CC7
SOFTWARE
PRO A:69 , ALA A:71 , MET A:111 , PRO A:364 , PRO A:365 , GLY A:368 , HOH A:712
BINDING SITE FOR RESIDUE GOL A 425
26
CC8
SOFTWARE
GLU A:80 , ARG A:82 , THR A:387 , HOH A:673
BINDING SITE FOR RESIDUE GOL A 426
27
CC9
SOFTWARE
VAL A:272 , LYS A:273 , GLY A:276 , ILE A:277 , VAL A:328
BINDING SITE FOR RESIDUE GOL A 427
28
DC1
SOFTWARE
LYS A:227 , ARG A:231 , HOH A:790
BINDING SITE FOR RESIDUE GOL A 428
29
DC2
SOFTWARE
LYS A:170 , THR A:261 , GLN A:263 , HOH A:553
BINDING SITE FOR RESIDUE GOL A 429
30
DC3
SOFTWARE
MET A:30 , ARG A:372 , GLU A:373 , ALA A:376 , HOH A:611 , HOH A:675
BINDING SITE FOR RESIDUE GOL A 430
31
DC4
SOFTWARE
GLN A:141 , LYS A:307 , SER A:337 , ARG A:347 , TRP A:362 , LYS A:369 , GLN A:381 , HOH A:540 , HOH A:608 , HOH A:639
BINDING SITE FOR RESIDUE GOL A 431
32
DC5
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:409
BINDING SITE FOR RESIDUE ORO A 432
33
DC6
SOFTWARE
ARG A:245 , HIS A:248 , HOH A:723
BINDING SITE FOR RESIDUE SO4 A 433
34
DC7
SOFTWARE
ARG A:160 , GLN A:325 , ACT A:439 , HOH A:762
BINDING SITE FOR RESIDUE SO4 A 434
35
DC8
SOFTWARE
ARG A:82 , VAL A:83 , LEU A:84 , GLY A:85 , ACT A:442 , HOH A:570
BINDING SITE FOR RESIDUE SO4 A 435
36
DC9
SOFTWARE
ARG A:249
BINDING SITE FOR RESIDUE SO4 A 436
37
EC1
SOFTWARE
GOL A:424 , HOH A:516
BINDING SITE FOR RESIDUE ACT A 437
38
EC2
SOFTWARE
GLN A:168 , ALA A:169 , THR A:172 , LEU A:205 , ASP A:207 , GOL A:420 , HOH A:522 , HOH A:600
BINDING SITE FOR RESIDUE ACT A 438
39
EC3
SOFTWARE
GLU A:103 , ARG A:160 , GOL A:414 , SO4 A:434 , HOH A:565 , HOH A:583 , HOH A:799
BINDING SITE FOR RESIDUE ACT A 439
40
EC4
SOFTWARE
SER A:64 , GLY A:66 , GLY A:107 , HOH A:679 , HOH A:802
BINDING SITE FOR RESIDUE ACT A 440
41
EC5
SOFTWARE
HOH A:547
BINDING SITE FOR RESIDUE ACT A 441
42
EC6
SOFTWARE
GLY A:85 , HIS A:86 , SO4 A:435
BINDING SITE FOR RESIDUE ACT A 442
43
EC7
SOFTWARE
GLU A:229 , ARG A:232
BINDING SITE FOR RESIDUE ACT A 443
[
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)
Exon 1.3 (A:80-146)
Exon 1.4 (A:146-174)
Exon 1.5 (A:174-236)
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
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
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_d3w7ra_ (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
d3w7ra_
A:
[
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:
Select:
Label:
Sorry, no Info available
[
close Pfam info
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(currently selected atoms:
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Chain A
Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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