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1XJB
Asym. Unit
Info
Asym.Unit (127 KB)
Biol.Unit 1 (120 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN TYPE 3 3ALPHA-HYDROXYSTEROID DEHYDROGENASE IN COMPLEX WITH NADP(H), CITRATE AND ACETATE MOLECULES
Authors
:
J. -F. Couture, K. Pereira De Jesus-Tran, A. -M. Roy, P. Legrand, L. Ca L. Cote, V. Luu-The, F. Labrie, R. Breton
Date
:
23 Sep 04 (Deposition) - 21 Jun 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Human 3Alphahds3; Aldo-Keto Reductase; Nadp; Induce-Fit Mecanism, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. -F. Couture, A. -M. Roy, L. Cantin, P. Legrand, V. Luu-The, F. Labrie R. Breton
Comparison Of Crystal Structures Of Human Type 3 3Alpha-Hydroxysteroid Dehydrogenase Reveals An "Induced-Fit Mechanism And A Conserved Basic Motif Involved In The Binding Of Androgen
Protein Sci. V. 14 1485 2005
[
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Hetero Components
(6, 11)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
2a: BETA-MERCAPTOETHANOL (BMEa)
3a: CITRIC ACID (CITa)
4a: 1,2-ETHANEDIOL (EDOa)
4b: 1,2-ETHANEDIOL (EDOb)
5a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
5b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
3
Ligand/Ion
ACETATE ION
2
BME
1
Ligand/Ion
BETA-MERCAPTOETHANOL
3
CIT
1
Ligand/Ion
CITRIC ACID
4
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
5
NAP
2
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
6
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
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 ACT A 1002
02
AC2
SOFTWARE
TYR A:55 , HIS A:117 , NAP A:1001 , CIT A:1006 , HOH A:5005
BINDING SITE FOR RESIDUE ACT A 5002
03
AC3
SOFTWARE
TYR B:55 , HIS B:117 , NAP B:5001 , HOH B:6191
BINDING SITE FOR RESIDUE ACT B 6002
04
AC4
SOFTWARE
ARG A:96 , ARG B:276
BINDING SITE FOR RESIDUE SO4 B 1004
05
AC5
SOFTWARE
ARG B:91 , HOH B:6067 , HOH B:6160
BINDING SITE FOR RESIDUE SO4 B 5004
06
AC6
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 , LEU A:268 , ALA A:269 , LYS A:270 , SER A:271 , TYR A:272 , ARG A:276 , GLN A:279 , ASN A:280 , ACT A:5002 , HOH A:5005 , HOH A:5017 , HOH A:5043 , HOH A:5063 , HOH A:5175 , HOH A:5198
BINDING SITE FOR RESIDUE NAP A 1001
07
AC7
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 , GLY B:220 , SER B:221 , HIS B:222 , LEU B:236 , ALA B:253 , LEU B:268 , LYS B:270 , SER B:271 , TYR B:272 , ARG B:276 , GLN B:279 , ASN B:280 , LEU B:306 , ACT B:6002 , HOH B:6022
BINDING SITE FOR RESIDUE NAP B 5001
08
AC8
SOFTWARE
TYR B:5 , GLN B:6 , PRO B:17 , VAL B:18 , LEU B:19 , GLY B:45 , PHE B:46 , HIS B:47 , HIS B:48 , PHE B:284
BINDING SITE FOR RESIDUE EDO B 1003
09
AC9
SOFTWARE
LYS A:123 , ASP A:140 , THR A:141 , HOH A:5252
BINDING SITE FOR RESIDUE EDO A 5003
10
BC1
SOFTWARE
TYR A:24 , VAL A:54 , TRP A:86 , HIS A:222 , TRP A:227 , LEU A:306 , ACT A:5002 , HOH A:5005 , HOH A:5223 , HOH A:5228
BINDING SITE FOR RESIDUE CIT A 1006
11
BC2
SOFTWARE
TYR A:5 , SER B:3 , TYR B:5 , CYS B:7
BINDING SITE FOR RESIDUE BME A 1005
[
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
[
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]
Exons
(9, 18)
Info
All Exons
Exon 1.4a (A:1-28 | 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:1-28
B:2-28
28
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_d1xjba_ (A:)
1b: SCOP_d1xjbb_ (B:)
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Folds
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(
)
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
d1xjba_
A:
1b
d1xjbb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1xjbB00 (B:2-323)
1b: CATH_1xjbA00 (A:-1-323)
View:
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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
1xjbB00
B:2-323
1b
1xjbA00
A:-1-323
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Aldo_ket_red_1xjbB01 (B:18-301)
1b: PFAM_Aldo_ket_red_1xjbB02 (B:18-301)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Aldo_ket_red]
(94)
Family
:
Aldo_ket_red
(94)
Homo sapiens (Human)
(60)
1a
Aldo_ket_red-1xjbB01
B:18-301
1b
Aldo_ket_red-1xjbB02
B:18-301
[
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