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1SIR
Asym. Unit
Info
Asym.Unit (71 KB)
Biol.Unit 1 (257 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE AND MECHANISM OF HUMAN GLUTARYL-COA DEHYDROGENASE
Authors
:
M. Wang, Z. Fu, R. Paschke, S. L. Goodman, F. E. Frerman, J. J. Kim
Date
:
01 Mar 04 (Deposition) - 07 Sep 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (4x)
Keywords
:
Acyl-Coa Dehydrogenase, Decoboxylation Flavin Protein, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Fu, M. Wang, R. Paschke, K. S. Rao, F. E. Frerman, J. J. Kim
Crystal Structures Of Human Glutaryl-Coa Dehydrogenase With And Without An Alternate Substrate: Structural Bases Of Dehydrogenation And Decarboxylation Reactions
Biochemistry V. 43 9674 2004
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2a: S-4-NITROBUTYRYL-COA (NBCa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
NBC
1
Ligand/Ion
S-4-NITROBUTYRYL-COA
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PHE A:133 , LEU A:135 , THR A:136 , GLY A:141 , SER A:142 , TRP A:168 , ILE A:169 , THR A:170 , LEU A:212 , ARG A:275 , PHE A:278 , LEU A:282 , ASN A:285 , GLN A:286 , ASP A:343 , MET A:344 , GLY A:347 , ILE A:350 , THR A:372 , PHE A:390 , NBC A:400 , HOH A:501 , HOH A:502 , HOH A:506
BINDING SITE FOR RESIDUE FAD A 399
2
AC2
SOFTWARE
ARG A:94 , SER A:95 , LEU A:103 , SER A:142 , PRO A:144 , THR A:170 , PHE A:243 , GLY A:244 , LEU A:246 , ASN A:247 , ARG A:250 , PRO A:320 , TYR A:369 , GLU A:370 , ARG A:382 , FAD A:399
BINDING SITE FOR RESIDUE NBC A 400
[
close Site info
]
SAPs(SNPs)/Variants
(60, 60)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_071510 (E20D, chain A, )
02: VAR_000366 (R44C, chain A, )
03: VAR_000367 (R50L, chain A, )
04: VAR_000368 (G57R, chain A, )
05: VAR_000369 (C71Y, chain A, )
06: VAR_000370 (A78V, chain A, )
07: VAR_000371 (R84G, chain A, )
08: VAR_000372 (R94G, chain A, )
09: VAR_000373 (S95L, chain A, )
10: VAR_000374 (V104I, chain A, )
11: VAR_000375 (R117Q, chain A, )
12: VAR_000376 (G134R, chain A, )
13: VAR_000377 (L135R, chain A, )
14: VAR_000378 (M147T, chain A, )
15: VAR_000379 (A151T, chain A, )
16: VAR_000380 (R183P, chain A, )
17: VAR_000381 (F192L, chain A, )
18: VAR_000382 (R213Q, chain A, )
19: VAR_000383 (R213W, chain A, )
20: VAR_060588 (M219V, chain A, )
21: VAR_000384 (M222V, chain A, )
22: VAR_071511 (G224V, chain A, )
23: VAR_000385 (P234S, chain A, )
24: VAR_000386 (L239P, chain A, )
25: VAR_000387 (A249T, chain A, )
26: VAR_000388 (R250W, chain A, )
27: VAR_000389 (Y251H, chain A, )
28: VAR_000390 (A254T, chain A, )
29: VAR_000391 (A254V, chain A, )
30: VAR_000392 (S261L, chain A, )
31: VAR_000393 (C264S, chain A, )
32: VAR_000394 (L265W, chain A, )
33: VAR_000395 (R269W, chain A, )
34: VAR_000396 (Q289E, chain A, )
35: VAR_000397 (A305T, chain A, )
36: VAR_000398 (G310R, chain A, )
37: VAR_000399 (G310S, chain A, )
38: VAR_000400 (R311C, chain A, )
39: VAR_000401 (R311H, chain A, )
40: VAR_000402 (E321K, chain A, )
41: VAR_000403 (C331R, chain A, )
42: VAR_000404 (A338T, chain A, )
43: VAR_000405 (R339C, chain A, )
44: VAR_000406 (R339H, chain A, )
45: VAR_000407 (R342Q, chain A, )
46: VAR_000409 (G346A, chain A, )
47: VAR_000408 (G346R, chain A, )
48: VAR_000410 (N348D, chain A, )
49: VAR_000411 (V356M, chain A, )
50: VAR_000413 (R358Q, chain A, )
51: VAR_000412 (R358W, chain A, )
52: VAR_000414 (H359R, chain A, )
53: VAR_000415 (N362K, chain A, )
54: VAR_000416 (L363P, chain A, )
55: VAR_000417 (E370K, chain A, )
56: VAR_000418 (T372I, chain A, )
57: VAR_000419 (A377T, chain A, )
58: VAR_000420 (A377V, chain A, )
59: VAR_000421 (T385M, chain A, )
60: VAR_000422 (A389E, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_071510
E
64
D
GCDH_HUMAN
Disease (GA1)
---
A
E
20
D
02
UniProt
VAR_000366
R
88
C
GCDH_HUMAN
Disease (GA1)
---
A
R
44
C
03
UniProt
VAR_000367
R
94
L
GCDH_HUMAN
Disease (GA1)
---
A
R
50
L
04
UniProt
VAR_000368
G
101
R
GCDH_HUMAN
Disease (GA1)
---
A
G
57
R
05
UniProt
VAR_000369
C
115
Y
GCDH_HUMAN
Disease (GA1)
---
A
C
71
Y
06
UniProt
VAR_000370
A
122
V
GCDH_HUMAN
Disease (GA1)
---
A
A
78
V
07
UniProt
VAR_000371
R
128
G
GCDH_HUMAN
Disease (GA1)
---
A
R
84
G
08
UniProt
VAR_000372
R
138
G
GCDH_HUMAN
Disease (GA1)
---
A
R
94
G
09
UniProt
VAR_000373
S
139
L
GCDH_HUMAN
Disease (GA1)
---
A
S
95
L
10
UniProt
VAR_000374
V
148
I
GCDH_HUMAN
Disease (GA1)
---
A
V
104
I
11
UniProt
VAR_000375
R
161
Q
GCDH_HUMAN
Disease (GA1)
---
A
R
117
Q
12
UniProt
VAR_000376
G
178
R
GCDH_HUMAN
Disease (GA1)
---
A
G
134
R
13
UniProt
VAR_000377
L
179
R
GCDH_HUMAN
Disease (GA1)
---
A
L
135
R
14
UniProt
VAR_000378
M
191
T
GCDH_HUMAN
Disease (GA1)
---
A
M
147
T
15
UniProt
VAR_000379
A
195
T
GCDH_HUMAN
Disease (GA1)
---
A
A
151
T
16
UniProt
VAR_000380
R
227
P
GCDH_HUMAN
Disease (GA1)
---
A
R
183
P
17
UniProt
VAR_000381
F
236
L
GCDH_HUMAN
Disease (GA1)
---
A
F
192
L
18
UniProt
VAR_000382
R
257
Q
GCDH_HUMAN
Disease (GA1)
---
A
R
213
Q
19
UniProt
VAR_000383
R
257
W
GCDH_HUMAN
Disease (GA1)
---
A
R
213
W
20
UniProt
VAR_060588
M
263
V
GCDH_HUMAN
Disease (GA1)
---
A
M
219
V
21
UniProt
VAR_000384
M
266
V
GCDH_HUMAN
Disease (GA1)
---
A
M
222
V
22
UniProt
VAR_071511
G
268
V
GCDH_HUMAN
Disease (GA1)
---
A
G
224
V
23
UniProt
VAR_000385
P
278
S
GCDH_HUMAN
Disease (GA1)
---
A
P
234
S
24
UniProt
VAR_000386
L
283
P
GCDH_HUMAN
Disease (GA1)
---
A
L
239
P
25
UniProt
VAR_000387
A
293
T
GCDH_HUMAN
Disease (GA1)
---
A
A
249
T
26
UniProt
VAR_000388
R
294
W
GCDH_HUMAN
Disease (GA1)
---
A
R
250
W
27
UniProt
VAR_000389
Y
295
H
GCDH_HUMAN
Disease (GA1)
---
A
Y
251
H
28
UniProt
VAR_000390
A
298
T
GCDH_HUMAN
Polymorphism
---
A
A
254
T
29
UniProt
VAR_000391
A
298
V
GCDH_HUMAN
Polymorphism
---
A
A
254
V
30
UniProt
VAR_000392
S
305
L
GCDH_HUMAN
Disease (GA1)
---
A
S
261
L
31
UniProt
VAR_000393
C
308
S
GCDH_HUMAN
Disease (GA1)
---
A
C
264
S
32
UniProt
VAR_000394
L
309
W
GCDH_HUMAN
Disease (GA1)
---
A
L
265
W
33
UniProt
VAR_000395
R
313
W
GCDH_HUMAN
Disease (GA1)
---
A
R
269
W
34
UniProt
VAR_000396
Q
333
E
GCDH_HUMAN
Disease (GA1)
---
A
Q
289
E
35
UniProt
VAR_000397
A
349
T
GCDH_HUMAN
Disease (GA1)
---
A
A
305
T
36
UniProt
VAR_000398
G
354
R
GCDH_HUMAN
Disease (GA1)
---
A
G
310
R
37
UniProt
VAR_000399
G
354
S
GCDH_HUMAN
Disease (GA1)
---
A
G
310
S
38
UniProt
VAR_000400
R
355
C
GCDH_HUMAN
Disease (GA1)
---
A
R
311
C
39
UniProt
VAR_000401
R
355
H
GCDH_HUMAN
Disease (GA1)
---
A
R
311
H
40
UniProt
VAR_000402
E
365
K
GCDH_HUMAN
Disease (GA1)
---
A
E
321
K
41
UniProt
VAR_000403
C
375
R
GCDH_HUMAN
Disease (GA1)
---
A
C
331
R
42
UniProt
VAR_000404
A
382
T
GCDH_HUMAN
Disease (GA1)
---
A
A
338
T
43
UniProt
VAR_000405
R
383
C
GCDH_HUMAN
Disease (GA1)
---
A
R
339
C
44
UniProt
VAR_000406
R
383
H
GCDH_HUMAN
Disease (GA1)
---
A
R
339
H
45
UniProt
VAR_000407
R
386
Q
GCDH_HUMAN
Disease (GA1)
---
A
R
342
Q
46
UniProt
VAR_000409
G
390
A
GCDH_HUMAN
Disease (GA1)
---
A
G
346
A
47
UniProt
VAR_000408
G
390
R
GCDH_HUMAN
Disease (GA1)
---
A
G
346
R
48
UniProt
VAR_000410
N
392
D
GCDH_HUMAN
Disease (GA1)
---
A
N
348
D
49
UniProt
VAR_000411
V
400
M
GCDH_HUMAN
Disease (GA1)
---
A
V
356
M
50
UniProt
VAR_000413
R
402
Q
GCDH_HUMAN
Disease (GA1)
---
A
R
358
Q
51
UniProt
VAR_000412
R
402
W
GCDH_HUMAN
Disease (GA1)
---
A
R
358
W
52
UniProt
VAR_000414
H
403
R
GCDH_HUMAN
Disease (GA1)
---
A
H
359
R
53
UniProt
VAR_000415
N
406
K
GCDH_HUMAN
Disease (GA1)
---
A
N
362
K
54
UniProt
VAR_000416
L
407
P
GCDH_HUMAN
Disease (GA1)
---
A
L
363
P
55
UniProt
VAR_000417
E
414
K
GCDH_HUMAN
Disease (GA1)
---
A
E
370
K
56
UniProt
VAR_000418
T
416
I
GCDH_HUMAN
Disease (GA1)
---
A
T
372
I
57
UniProt
VAR_000419
A
421
T
GCDH_HUMAN
Disease (GA1)
151201155
A
A
377
T
58
UniProt
VAR_000420
A
421
V
GCDH_HUMAN
Disease (GA1)
---
A
A
377
V
59
UniProt
VAR_000421
T
429
M
GCDH_HUMAN
Disease (GA1)
---
A
T
385
M
60
UniProt
VAR_000422
A
433
E
GCDH_HUMAN
Disease (GA1)
---
A
A
389
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: ACYL_COA_DH_1 (A:134-146)
2: ACYL_COA_DH_2 (A:343-362)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ACYL_COA_DH_1
PS00072
Acyl-CoA dehydrogenases signature 1.
GCDH_HUMAN
178-190
1
A:134-146
2
ACYL_COA_DH_2
PS00073
Acyl-CoA dehydrogenases signature 2.
GCDH_HUMAN
387-406
1
A:343-362
[
close PROSITE info
]
Exons
(9, 9)
Info
All Exons
Exon 1.4 (A:3-47)
Exon 1.5 (A:47-68)
Exon 1.7 (A:68-125)
Exon 1.8 (A:125-168)
Exon 1.9a (A:168-240)
Exon 1.10 (A:241-275)
Exon 1.11 (A:275-317)
Exon 1.12 (A:317-371)
Exon 1.13a (A:371-392)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.3/1.4
02: Boundary 1.4/1.5
03: Boundary 1.5/1.7
04: Boundary 1.7/1.8
05: Boundary 1.8/1.9a
06: Boundary 1.9a/1.10
07: Boundary 1.10/1.11
08: Boundary 1.11/1.12
09: Boundary 1.12/1.13a
10: Boundary 1.13a/-
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
ENST00000222214
1
ENSE00001409053
chr19:
13001974-13002016
43
GCDH_HUMAN
-
0
0
-
-
1.2
ENST00000222214
2
ENSE00002191084
chr19:
13002085-13002209
125
GCDH_HUMAN
1-31
31
0
-
-
1.3
ENST00000222214
3
ENSE00001597102
chr19:
13002301-13002336
36
GCDH_HUMAN
31-43
13
0
-
-
1.4
ENST00000222214
4
ENSE00001685900
chr19:
13002645-13002788
144
GCDH_HUMAN
43-91
49
1
A:3-47
45
1.5
ENST00000222214
5
ENSE00001695685
chr19:
13002930-13002992
63
GCDH_HUMAN
91-112
22
1
A:47-68
22
1.7
ENST00000222214
7
ENSE00001685991
chr19:
13004297-13004467
171
GCDH_HUMAN
112-169
58
1
A:68-125
58
1.8
ENST00000222214
8
ENSE00001668484
chr19:
13006806-13006935
130
GCDH_HUMAN
169-212
44
1
A:125-168
44
1.9a
ENST00000222214
9a
ENSE00000682677
chr19:
13007019-13007235
217
GCDH_HUMAN
212-284
73
1
A:168-240
73
1.10
ENST00000222214
10
ENSE00000682676
chr19:
13007724-13007827
104
GCDH_HUMAN
285-319
35
1
A:241-275
35
1.11
ENST00000222214
11
ENSE00000682675
chr19:
13008117-13008242
126
GCDH_HUMAN
319-361
43
1
A:275-317
43
1.12
ENST00000222214
12
ENSE00000682672
chr19:
13008517-13008677
161
GCDH_HUMAN
361-415
55
1
A:317-371
55
1.13a
ENST00000222214
13a
ENSE00001335835
chr19:
13010282-13010782
501
GCDH_HUMAN
415-438
24
1
A:371-392
22
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1sira1 (A:239-392)
2a: SCOP_d1sira2 (A:3-238)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Acyl-CoA dehydrogenase C-terminal domain-like
(61)
Family
:
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain
(29)
Protein domain
:
Glutaryl-CoA dehydrogenase GCDH
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d1sira1
A:239-392
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Superfamily
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Family
:
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains
(32)
Protein domain
:
Glutaryl-CoA dehydrogenase GCDH
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
2a
d1sira2
A:3-238
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1sirA01 (A:3-130)
2a: CATH_1sirA03 (A:238-392)
3a: CATH_1sirA02 (A:131-237)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Butyryl-Coa Dehydrogenase, subunit A; domain 1
(28)
Homologous Superfamily
:
Butyryl-Coa Dehydrogenase, subunit A, domain 1
(28)
Human (Homo sapiens)
(10)
1a
1sirA01
A:3-130
Architecture
:
Up-down Bundle
(3216)
Topology
:
Butyryl-CoA Dehydrogenase, subunit A; domain 3
(76)
Homologous Superfamily
:
Butyryl-CoA Dehydrogenase, subunit A, domain 3
(37)
Human (Homo sapiens)
(13)
2a
1sirA03
A:238-392
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Butyryl-CoA Dehydrogenase, subunit A; domain 2
(35)
Homologous Superfamily
:
Butyryl-CoA Dehydrogenase, subunit A, domain 2
(35)
Human (Homo sapiens)
(14)
3a
1sirA02
A:131-237
[
close CATH info
]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Acyl_CoA_dh_1_1sirA01 (A:243-385)
2a: PFAM_Acyl_CoA_dh_M_1sirA02 (A:132-186)
3a: PFAM_Acyl_CoA_dh_N_1sirA03 (A:17-128)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
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(
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Clan
:
Acyl-CoA_dh
(32)
Family
:
Acyl-CoA_dh_1
(24)
Homo sapiens (Human)
(10)
1a
Acyl-CoA_dh_1-1sirA01
A:243-385
Clan
:
no clan defined [family: Acyl-CoA_dh_M]
(24)
Family
:
Acyl-CoA_dh_M
(24)
Homo sapiens (Human)
(10)
2a
Acyl-CoA_dh_M-1sirA02
A:132-186
Clan
:
no clan defined [family: Acyl-CoA_dh_N]
(23)
Family
:
Acyl-CoA_dh_N
(23)
Homo sapiens (Human)
(10)
3a
Acyl-CoA_dh_N-1sirA03
A:17-128
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