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3BUR
Asym. Unit
Info
Asym.Unit (126 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (62 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DELTA(4)-3-KETOSTEROID 5-BETA-REDUCTASE IN COMPLEX WITH NADP AND TESTOSTERONE. RESOLUTION: 1.62 A.
Authors
:
L. Di Costanzo, D. W. Christianson
Date
:
03 Jan 08 (Deposition) - 01 Apr 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.62
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
5Beta-Reductase; Catalytic Tetrad; Testosterone; Nadp, Bile Acid Catabolism, Disease Mutation, Lipid Metabolism, Oxidoreductase, Steroid Metabolism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Di Costanzo, J. E. Drury, T. M. Penning, D. W. Christianson
Crystal Structure Of Human Liver {Delta}4-3-Ketosteroid 5{Beta}-Reductase (Akr1D1) And Implications For Substrate Binding And Catalysis.
J. Biol. Chem. V. 283 16830 2008
[
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Hetero Components
(3, 14)
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)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
3a: TESTOSTERONE (TESa)
3b: TESTOSTERONE (TESb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
10
Ligand/Ion
GLYCEROL
2
NAP
2
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3
TES
2
Ligand/Ion
TESTOSTERONE
[
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Sites
(14, 14)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY B:24 , THR B:25 , TYR B:26 , ASP B:53 , TYR B:58 , SER B:169 , ASN B:170 , GLN B:193 , TYR B:219 , SER B:220 , PRO B:221 , LEU B:222 , GLY B:223 , THR B:224 , SER B:225 , LEU B:239 , ALA B:256 , ILE B:271 , PRO B:272 , LYS B:273 , SER B:274 , PHE B:275 , ARG B:279 , GLU B:282 , ASN B:283 , HOH B:1062 , HOH B:1067 , HOH B:1162 , HOH B:1367 , HOH B:1410 , HOH B:1476
BINDING SITE FOR RESIDUE NAP B 327
02
AC2
SOFTWARE
GLY A:24 , THR A:25 , TYR A:26 , ASP A:53 , TYR A:58 , LYS A:87 , SER A:169 , ASN A:170 , GLN A:193 , TYR A:219 , SER A:220 , PRO A:221 , LEU A:222 , GLY A:223 , THR A:224 , SER A:225 , LEU A:239 , ALA A:256 , ILE A:271 , PRO A:272 , LYS A:273 , SER A:274 , PHE A:275 , ARG A:279 , GLU A:282 , ASN A:283 , HOH A:1042 , HOH A:1082 , HOH A:1229 , HOH A:1252 , HOH A:1315 , HOH A:1486
BINDING SITE FOR RESIDUE NAP A 328
03
AC3
SOFTWARE
TYR A:26 , ILE A:57 , TRP A:89 , TYR A:132 , SER A:225 , ARG A:226 , ASN A:227 , TRP A:230
BINDING SITE FOR RESIDUE TES A 339
04
AC4
SOFTWARE
TYR B:26 , ILE B:57 , TRP B:89 , TYR B:132 , THR B:224 , SER B:225 , ARG B:226 , ASN B:227 , TRP B:230 , HOH B:1367
BINDING SITE FOR RESIDUE TES B 340
05
AC5
SOFTWARE
GLU A:103 , ARG A:107 , LEU A:111 , ASP B:129 , HOH B:1078
BINDING SITE FOR RESIDUE GOL B 329
06
AC6
SOFTWARE
THR B:224 , SER B:225 , ARG B:226 , HOH B:1457
BINDING SITE FOR RESIDUE GOL B 330
07
AC7
SOFTWARE
ARG A:134 , ILE A:229 , TRP A:230
BINDING SITE FOR RESIDUE GOL A 331
08
AC8
SOFTWARE
THR A:224 , SER A:225 , ARG A:226 , LEU A:239 , HOH A:1486
BINDING SITE FOR RESIDUE GOL A 332
09
AC9
SOFTWARE
ASP A:112 , HOH A:1131 , MET B:97 , PRO B:100 , THR B:101 , ARG B:104
BINDING SITE FOR RESIDUE GOL A 333
10
BC1
SOFTWARE
SER A:225
BINDING SITE FOR RESIDUE GOL A 334
11
BC2
SOFTWARE
LEU A:106 , ARG A:107 , GLN A:110 , LEU A:111 , HOH A:1032 , LEU B:243 , ASP B:298
BINDING SITE FOR RESIDUE GOL A 335
12
BC3
SOFTWARE
ARG B:279
BINDING SITE FOR RESIDUE GOL B 336
13
BC4
SOFTWARE
ARG A:99 , GLU A:103 , LEU A:162 , HOH A:1123 , TYR B:56 , ARG B:104 , ASP B:129 , HOH B:1339
BINDING SITE FOR RESIDUE GOL B 337
14
BC5
SOFTWARE
ARG A:279
BINDING SITE FOR RESIDUE GOL A 338
[
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]
SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_033007 (L106F, chain A/B, )
2: VAR_044430 (P133R, chain A/B, )
3: VAR_033008 (P198L, chain A/B, )
4: VAR_044431 (R261C, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_033007
L
106
F
AK1D1_HUMAN
Disease (CBAS2)
---
A/B
L
106
F
2
UniProt
VAR_044430
P
133
R
AK1D1_HUMAN
Disease (CBAS2)
---
A/B
P
133
R
3
UniProt
VAR_033008
P
198
L
AK1D1_HUMAN
Disease (CBAS2)
---
A/B
P
198
L
4
UniProt
VAR_044431
R
261
C
AK1D1_HUMAN
Disease (CBAS2)
---
A/B
R
261
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: ALDOKETO_REDUCTASE_1 (A:48-65,B:48-65)
2: ALDOKETO_REDUCTASE_2 (A:154-171,B:154-171)
3: ALDOKETO_REDUCTASE_3 (A:271-286,B:271-286)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALDOKETO_REDUCTASE_1
PS00798
Aldo/keto reductase family signature 1.
AK1D1_HUMAN
48-65
2
A:48-65
B:48-65
2
ALDOKETO_REDUCTASE_2
PS00062
Aldo/keto reductase family signature 2.
AK1D1_HUMAN
154-171
2
A:154-171
B:154-171
3
ALDOKETO_REDUCTASE_3
PS00063
Aldo/keto reductase family putative active site signature.
AK1D1_HUMAN
271-286
2
A:271-286
B:271-286
[
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3bura_ (A:)
1b: SCOP_d3burb_ (B:)
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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
:
automated matches
(62)
Human (Homo sapiens) [TaxId: 9606]
(48)
1a
d3bura_
A:
1b
d3burb_
B:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3burA00 (A:2-326)
1b: CATH_3burB00 (B:2-326)
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(
)
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
3burA00
A:2-326
1b
3burB00
B:2-326
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (126 KB)
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