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Getting 'Biological Unit' information from database.
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3BUR
Biol. Unit 1
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, 8)
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
6
Ligand/Ion
GLYCEROL
2
NAP
1
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3
TES
1
Ligand/Ion
TESTOSTERONE
[
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Sites
(10, 10)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC8 (SOFTWARE)
06: AC9 (SOFTWARE)
07: BC1 (SOFTWARE)
08: BC2 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC5 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
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
02
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
03
AC5
SOFTWARE
GLU A:103 , ARG A:107 , LEU A:111 , ASP B:129 , HOH B:1078
BINDING SITE FOR RESIDUE GOL B 329
04
AC7
SOFTWARE
ARG A:134 , ILE A:229 , TRP A:230
BINDING SITE FOR RESIDUE GOL A 331
05
AC8
SOFTWARE
THR A:224 , SER A:225 , ARG A:226 , LEU A:239 , HOH A:1486
BINDING SITE FOR RESIDUE GOL A 332
06
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
07
BC1
SOFTWARE
SER A:225
BINDING SITE FOR RESIDUE GOL A 334
08
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
09
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
10
BC5
SOFTWARE
ARG A:279
BINDING SITE FOR RESIDUE GOL A 338
[
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SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_033007 (L106F, chain A, )
2: VAR_044430 (P133R, chain A, )
3: VAR_033008 (P198L, chain A, )
4: VAR_044431 (R261C, chain A, )
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
L
106
F
2
UniProt
VAR_044430
P
133
R
AK1D1_HUMAN
Disease (CBAS2)
---
A
P
133
R
3
UniProt
VAR_033008
P
198
L
AK1D1_HUMAN
Disease (CBAS2)
---
A
P
198
L
4
UniProt
VAR_044431
R
261
C
AK1D1_HUMAN
Disease (CBAS2)
---
A
R
261
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: ALDOKETO_REDUCTASE_1 (A:48-65)
2: ALDOKETO_REDUCTASE_2 (A:154-171)
3: ALDOKETO_REDUCTASE_3 (A: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
1
A:48-65
-
2
ALDOKETO_REDUCTASE_2
PS00062
Aldo/keto reductase family signature 2.
AK1D1_HUMAN
154-171
1
A:154-171
-
3
ALDOKETO_REDUCTASE_3
PS00063
Aldo/keto reductase family putative active site signature.
AK1D1_HUMAN
271-286
1
A:271-286
-
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3bura_ (A:)
1b: SCOP_d3burb_ (B:)
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Protein Domains
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(
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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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)
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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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Sorry, no Info available
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Atom Selection
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Protein
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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Example Commands
Example Command
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Show PDB file:
Asym.Unit (126 KB)
Header - Asym.Unit
Biol.Unit 1 (62 KB)
Header - Biol.Unit 1
Biol.Unit 2 (62 KB)
Header - Biol.Unit 2
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