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3RQS
Asym. Unit
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Asym.Unit (220 KB)
Biol.Unit 1 (214 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN L-3- HYDROXYACYL-COA DEHYDROGENASE (EC1.1.1.35) FROM MITOCHONDRIA AT THE RESOLUTION 2.0 A, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR487, MITOCHONDRIAL PROTEIN PARTNERSHIP
Authors
:
A. Kuzin, M. Su, J. Seetharaman, P. Patel, R. Xiao, C. Ciccosanti, R. Sha J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J Northeast Structural Genomics Consortium (Nesg), Mitochondri Protein Partnership (Mpp)
Date
:
28 Apr 11 (Deposition) - 25 May 11 (Release) - 03 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Structural Genomics, Psi-Biology, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Oxidoreductase, Mitochondrial Protein Partnership, Mpp
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Kuzin, M. Su, J. Seetharaman, P. Patel, R. Xiao, C. Ciccosanti, R. Shastry, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt
Northeast Structural Genomics Consortium Target Hr487
To Be Published
[
close entry info
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Hetero Components
(2, 23)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
2a: SELENOMETHIONINE (MSEa)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
7
Ligand/Ion
GLYCEROL
2
MSE
16
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:220 , VAL A:224 , VAL A:265 , THR A:269 , THR A:270 , ILE A:273 , GOL A:316 , HOH A:373
BINDING SITE FOR RESIDUE GOL A 315
2
AC2
SOFTWARE
ASN A:173 , TYR A:264 , GOL A:315 , GOL A:317 , HOH A:371 , GLY B:251
BINDING SITE FOR RESIDUE GOL A 316
3
AC3
SOFTWARE
MSE A:178 , PRO A:255 , MSE A:256 , LEU A:261 , GOL A:316 , HOH A:385 , ALA B:252 , HOH B:423
BINDING SITE FOR RESIDUE GOL A 317
4
AC4
SOFTWARE
PRO A:86 , LYS A:87 , GLU A:140 , ARG A:165 , LYS A:192 , HOH A:382
BINDING SITE FOR RESIDUE GOL A 318
5
AC5
SOFTWARE
ASN B:220 , VAL B:224 , VAL B:265 , THR B:269 , THR B:270 , ILE B:273 , GOL B:317 , HOH B:368 , HOH B:531 , HOH B:552
BINDING SITE FOR RESIDUE GOL B 315
6
AC6
SOFTWARE
MSE B:38 , ALA B:119 , ILE B:120 , GLU B:122 , ASN B:147 , HOH B:332 , HOH B:354 , HOH B:449 , HOH B:524
BINDING SITE FOR RESIDUE GOL B 316
7
AC7
SOFTWARE
GLY A:251 , HOH A:394 , PHE B:172 , ASN B:173 , LEU B:223 , VAL B:265 , GOL B:315 , HOH B:356
BINDING SITE FOR RESIDUE GOL B 317
[
close Site info
]
SAPs(SNPs)/Variants
(5, 10)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_024079 (A40T, chain A/B, )
2: VAR_024080 (D57E, chain A/B, )
3: VAR_026764 (P86P, chain A/B, )
4: VAR_055701 (Q152H, chain A/B, )
5: VAR_024081 (P258L, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_024079
A
40
T
HCDH_HUMAN
Disease (HADH deficiency)
---
A/B
A
40
T
2
UniProt
VAR_024080
D
57
E
HCDH_HUMAN
Disease (HADH deficiency)
---
A/B
D
57
E
3
UniProt
VAR_026764
L
86
P
HCDH_HUMAN
Polymorphism
4956145
A/B
P
86
P
4
UniProt
VAR_055701
Q
152
H
HCDH_HUMAN
Polymorphism
1051519
A/B
Q
152
H
5
UniProt
VAR_024081
P
258
L
HCDH_HUMAN
Disease (HHF4)
---
A/B
P
258
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: 3HCDH (A:213-237,B:213-237)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
3HCDH
PS00067
3-hydroxyacyl-CoA dehydrogenase signature.
HCDH_HUMAN
213-237
2
A:213-237
B:213-237
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.1c (A:23-44 | B:1-44)
Exon 1.4 (A:45-87 | B:45-87)
Exon 1.5a (A:88-140 | B:88-140)
Exon 1.6 (A:140-182 | B:140-182)
Exon 1.7 (A:183-212 | B:183-212)
Exon 1.8b (A:213-237 | B:213-237)
Exon 1.10b (A:237-276 | B:237-276)
Exon 1.11d (A:276-314 | B:276-314)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1c
2: Boundary 1.1c/1.4
3: Boundary 1.4/1.5a
4: Boundary 1.5a/1.6
5: Boundary 1.6/1.7
6: Boundary 1.7/1.8b
7: Boundary 1.8b/1.10b
8: Boundary 1.10b/1.11d
9: Boundary 1.11d/-
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
1.1c
ENST00000309522
1c
ENSE00001196027
chr4:
108910940-108911220
281
HCDH_HUMAN
1-44
44
2
A:23-44
B:1-44
22
44
1.4
ENST00000309522
4
ENSE00000333879
chr4:
108930915-108931043
129
HCDH_HUMAN
45-87
43
2
A:45-87
B:45-87
43
43
1.5a
ENST00000309522
5a
ENSE00000841666
chr4:
108935587-108935744
158
HCDH_HUMAN
88-140
53
2
A:88-140
B:88-140
53
53
1.6
ENST00000309522
6
ENSE00000841667
chr4:
108940696-108940822
127
HCDH_HUMAN
140-182
43
2
A:140-182
B:140-182
43
43
1.7
ENST00000309522
7
ENSE00000841668
chr4:
108944630-108944719
90
HCDH_HUMAN
183-212
30
2
A:183-212
B:183-212
30
30
1.8b
ENST00000309522
8b
ENSE00000841669
chr4:
108948844-108948916
73
HCDH_HUMAN
213-237
25
2
A:213-237
B:213-237
25
25
1.10b
ENST00000309522
10b
ENSE00000841670
chr4:
108954332-108954448
117
HCDH_HUMAN
237-276
40
2
A:237-276
B:237-276
40
40
1.11d
ENST00000309522
11d
ENSE00001561694
chr4:
108955395-108956331
937
HCDH_HUMAN
276-314
39
2
A:276-314
B:276-314
39
39
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3rqsa2 (A:216-314)
2a: SCOP_d3rqsa1 (A:23-215)
View:
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Label:
Classes
(
)
(
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Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
automated matches
(50)
Protein domain
:
automated matches
(50)
Human (Homo sapiens) [TaxId: 9606]
(13)
1a
d3rqsa2
A:216-314
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
6-phosphogluconate dehydrogenase-like, N-terminal domain
(69)
Protein domain
:
automated matches
(2)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d3rqsa1
A:23-215
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_3HCDH_3rqsB01 (B:216-313)
1b: PFAM_3HCDH_3rqsB02 (B:216-313)
2a: PFAM_3HCDH_N_3rqsB03 (B:29-214)
2b: PFAM_3HCDH_N_3rqsB04 (B:29-214)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6PGD_C
(47)
Family
:
3HCDH
(12)
Homo sapiens (Human)
(4)
1a
3HCDH-3rqsB01
B:216-313
1b
3HCDH-3rqsB02
B:216-313
Clan
:
NADP_Rossmann
(1239)
Family
:
3HCDH_N
(12)
Homo sapiens (Human)
(4)
2a
3HCDH_N-3rqsB03
B:29-214
2b
3HCDH_N-3rqsB04
B:29-214
[
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]
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Asymmetric Unit 1
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