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2HDJ
Asym. Unit
Info
Asym.Unit (127 KB)
Biol.Unit 1 (63 KB)
Biol.Unit 2 (62 KB)
Biol.Unit 3 (179 KB)
Biol.Unit 4 (123 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN TYPE 3 3ALPHA-HYDROXYSTEROID DEHYDROGENASE IN COMPLEX WITH NADP(H)
Authors
:
F. Faucher, K. Pereira De Jesus-Tran, L. Cantin, V. Luu-The, F. Labrie, R. Breton
Date
:
20 Jun 06 (Deposition) - 05 Dec 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: B (3x)
Biol. Unit 4: A (2x)
Keywords
:
Human 3Alphahds3, Aldo-Keto Reductase, Nadph, Akr, Akr1C2, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Faucher, K. Pereira De Jesus-Tran, L. Cantin, V. Luu-The, F. Labrie, R. Breton
Crystal Structures Of Mouse 17Alpha-Hydroxysteroid Dehydrogenase (Apoenzyme And Enzyme-Nadp(H) Binary Complex): Identification Of Molecular Determinants Responsible For The Unique 17Alpha-Reductive Activity Of This Enzyme.
J. Mol. Biol. V. 364 747 2006
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
2a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
2b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
2
NDP
2
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:39 , LYS A:68 , HOH A:805 , HOH A:806 , HOH A:830 , HOH A:874
BINDING SITE FOR RESIDUE SO4 A 401
02
AC2
SOFTWARE
ARG B:91 , HOH B:665 , HOH B:800
BINDING SITE FOR RESIDUE SO4 B 402
03
AC3
SOFTWARE
ARG A:96 , ARG B:276 , HOH B:717
BINDING SITE FOR RESIDUE SO4 B 403
04
AC4
SOFTWARE
ASP B:109 , ALA B:157 , GLY B:158 , LEU B:159
BINDING SITE FOR RESIDUE SO4 B 404
05
AC5
SOFTWARE
GLY A:22 , THR A:23 , TYR A:24 , ASP A:50 , TYR A:55 , LYS A:84 , HIS A:117 , SER A:166 , ASN A:167 , GLN A:190 , TYR A:216 , SER A:217 , ALA A:218 , LEU A:219 , GLY A:220 , SER A:221 , HIS A:222 , LEU A:236 , ALA A:253 , ALA A:269 , LYS A:270 , SER A:271 , TYR A:272 , ARG A:276 , GLN A:279 , ASN A:280 , EDO A:604 , HOH A:693 , HOH A:747 , HOH A:772 , HOH A:871
BINDING SITE FOR RESIDUE NDP A 501
06
AC6
SOFTWARE
GLY B:22 , THR B:23 , TYR B:24 , ASP B:50 , TYR B:55 , LYS B:84 , HIS B:117 , SER B:166 , ASN B:167 , GLN B:190 , TYR B:216 , SER B:217 , ALA B:218 , LEU B:219 , SER B:221 , HIS B:222 , LEU B:236 , ALA B:253 , LYS B:270 , SER B:271 , TYR B:272 , ASN B:273 , ARG B:276 , GLN B:279 , ASN B:280 , EDO B:603 , HOH B:681 , HOH B:715 , HOH B:814 , HOH B:835 , HOH B:838
BINDING SITE FOR RESIDUE NDP B 501
07
AC7
SOFTWARE
PRO B:92 , ALA B:146 , GLU B:149 , ALA B:150 , LYS B:153 , HOH B:710 , HOH B:859
BINDING SITE FOR RESIDUE EDO B 601
08
AC8
SOFTWARE
GLN B:6 , PRO B:17 , VAL B:18 , LEU B:19 , GLY B:45 , HIS B:47 , PHE B:284
BINDING SITE FOR RESIDUE EDO B 602
09
AC9
SOFTWARE
TYR B:24 , HIS B:222 , LEU B:306 , NDP B:501 , HOH B:715 , HOH B:836
BINDING SITE FOR RESIDUE EDO B 603
10
BC1
SOFTWARE
HIS A:222 , NDP A:501 , HOH A:781 , HOH A:871
BINDING SITE FOR RESIDUE EDO A 604
11
BC2
SOFTWARE
LYS A:123 , ASP A:140 , THR A:141
BINDING SITE FOR RESIDUE EDO A 605
12
BC3
SOFTWARE
GLN A:6 , PRO A:17 , VAL A:18 , LEU A:19 , GLY A:45 , HIS A:47 , PHE A:284
BINDING SITE FOR RESIDUE EDO A 606
[
close Site info
]
SAPs(SNPs)/Variants
(6, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_048216 (F46Y, chain A/B, )
2: VAR_066632 (I79V, chain A/B, )
3: VAR_066633 (H90Q, chain A/B, )
4: VAR_014748 (L172Q, chain A/B, )
5: VAR_066634 (H222Q, chain A/B, )
6: VAR_066635 (N300T, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_048216
F
46
Y
AK1C2_HUMAN
Polymorphism
2854482
A/B
F
46
Y
2
UniProt
VAR_066632
I
79
V
AK1C2_HUMAN
Disease (SRXY8)
---
A/B
I
79
V
3
UniProt
VAR_066633
H
90
Q
AK1C2_HUMAN
Disease (SRXY8)
---
A/B
H
90
Q
4
UniProt
VAR_014748
L
172
Q
AK1C2_HUMAN
Polymorphism
11474
A/B
L
172
Q
5
UniProt
VAR_066634
H
222
Q
AK1C2_HUMAN
Disease (SRXY8)
---
A/B
H
222
Q
6
UniProt
VAR_066635
N
300
T
AK1C2_HUMAN
Disease (SRXY8)
---
A/B
N
300
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ALDOKETO_REDUCTASE_2 (A:151-168,B:151-168)
2: ALDOKETO_REDUCTASE_3 (A:268-283,B:268-283)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALDOKETO_REDUCTASE_2
PS00062
Aldo/keto reductase family signature 2.
AK1C2_HUMAN
151-168
2
A:151-168
B:151-168
2
ALDOKETO_REDUCTASE_3
PS00063
Aldo/keto reductase family putative active site signature.
AK1C2_HUMAN
268-283
2
A:268-283
B:268-283
[
close PROSITE info
]
Exons
(9, 18)
Info
All Exons
Exon 1.4a (A:2-28 | B:2-28)
Exon 1.5 (A:29-84 | B:29-84)
Exon 1.6b (A:85-123 | B:85-123)
Exon 1.6e (A:124-149 | B:124-149)
Exon 1.7b (A:150-190 | B:150-190)
Exon 1.8 (A:191-227 | B:191-227)
Exon 1.9b (A:227-282 | B:227-282)
Exon 1.10a (A:283-310 | B:283-310)
Exon 1.11c (A:310-323 | B:310-323)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.4a
02: Boundary 1.4a/1.5
03: Boundary 1.5/1.6b
04: Boundary 1.6b/1.6e
05: Boundary 1.6e/1.7b
06: Boundary 1.7b/1.8
07: Boundary 1.8/1.9b
08: Boundary 1.9b/1.10a
09: Boundary 1.10a/1.11c
10: Boundary 1.11c/-
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
1.4a
ENST00000380753
4a
ENSE00002187446
chr10:
5046215-5045944
272
AK1C2_HUMAN
1-28
28
2
A:2-28
B:2-28
27
27
1.5
ENST00000380753
5
ENSE00001613313
chr10:
5043873-5043706
168
AK1C2_HUMAN
29-84
56
2
A:29-84
B:29-84
56
56
1.6b
ENST00000380753
6b
ENSE00001619656
chr10:
5042858-5042742
117
AK1C2_HUMAN
85-123
39
2
A:85-123
B:85-123
39
39
1.6e
ENST00000380753
6e
ENSE00001705571
chr10:
5041469-5041392
78
AK1C2_HUMAN
124-149
26
2
A:124-149
B:124-149
26
26
1.7b
ENST00000380753
7b
ENSE00001693200
chr10:
5040939-5040817
123
AK1C2_HUMAN
150-190
41
2
A:150-190
B:150-190
41
41
1.8
ENST00000380753
8
ENSE00001714710
chr10:
5038057-5037948
110
AK1C2_HUMAN
191-227
37
2
A:191-227
B:191-227
37
37
1.9b
ENST00000380753
9b
ENSE00001785365
chr10:
5037676-5037511
166
AK1C2_HUMAN
227-282
56
2
A:227-282
B:227-282
56
56
1.10a
ENST00000380753
10a
ENSE00001601494
chr10:
5034105-5034023
83
AK1C2_HUMAN
283-310
28
2
A:283-310
B:283-310
28
28
1.11c
ENST00000380753
11c
ENSE00001895645
chr10:
5032230-5029967
2264
AK1C2_HUMAN
310-323
14
2
A:310-323
B:310-323
14
14
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2hdja_ (A:)
1b: SCOP_d2hdjb_ (B:)
View:
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Label:
Classes
(
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(
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Folds
(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
NAD(P)-linked oxidoreductase
(286)
Family
:
Aldo-keto reductases (NADP)
(251)
Protein domain
:
3-alpha-hydroxysteroid dehydrogenase
(15)
Human (Homo sapiens), type III [TaxId: 9606]
(12)
1a
d2hdja_
A:
1b
d2hdjb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2hdjA00 (A:2-323)
1b: CATH_2hdjB00 (B:2-323)
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Classes
(
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(
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Topologies
(
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
NADP-dependent oxidoreductase
(181)
Human (Homo sapiens)
(116)
1a
2hdjA00
A:2-323
1b
2hdjB00
B:2-323
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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