PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2FVL
Asym. Unit
Info
Asym.Unit (185 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (61 KB)
Biol.Unit 3 (62 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN 3-ALPHA HYDROXYSTEROID/DIHYDRODIOL DEHYDROGENASE (AKR1C4) COMPLEXED WITH NADP+
Authors
:
E. Ugochukwu, C. Smee, K. Guo, P. Lukacik, K. Kavanagh, J. E. Debreczeni Delft, J. Weigelt, M. Sundstrom, C. Arrowsmith, A. Edwards, U. Opperm Structural Genomics Consortium (Sgc)
Date
:
31 Jan 06 (Deposition) - 21 Feb 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Chlordecone Reductase, Aldo-Keto Reductase, 3Alpha-Hsd1, Dd4, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Ugochukwu, C. Smee, K. Guo, P. Lukacik, K. Kavanagh, J. E. Debreczeni, F. Von Delft, J. Weigelt, M. Sundstrom, C. Arrowsmith, A. Edwards, U. Oppermann
Crystal Structure Of Human 3-Alpha Hydroxysteroid/Dihydrodiol Dehydrogenase (Akr1C4) Complexed With Nadp+
To Be Published
[
close entry info
]
Hetero Components
(1, 3)
Info
All Hetero Components
1a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
1b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
1c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAP
3
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:22 , THR A:23 , TYR A:24 , ASP A:50 , TYR A:55 , HIS A:117 , SER A:166 , ASN A:167 , GLN A:190 , HIS A:216 , SER A:217 , ALA A:218 , LEU A:219 , GLY A:220 , THR A:221 , GLN A:222 , ALA A:253 , LEU A:268 , LYS A:270 , SER A:271 , TYR A:272 , ARG A:276 , GLU A:279 , ASN A:280 , HOH A:1052 , HOH A:1059 , HOH A:1084 , HOH A:1102 , HOH A:1232 , HOH A:1262 , HOH C:1169 , HOH C:1210
BINDING SITE FOR RESIDUE NAP A 1001
2
AC2
SOFTWARE
GLY C:22 , THR C:23 , TYR C:24 , ASP C:50 , TYR C:55 , HIS C:117 , SER C:166 , ASN C:167 , GLN C:190 , HIS C:216 , SER C:217 , ALA C:218 , LEU C:219 , GLY C:220 , THR C:221 , GLN C:222 , ALA C:253 , LEU C:268 , LYS C:270 , SER C:271 , TYR C:272 , ARG C:276 , GLU C:279 , ASN C:280 , HOH C:1015 , HOH C:1018 , HOH C:1042 , HOH C:1123 , HOH C:1156 , HOH C:1179 , HOH C:1279
BINDING SITE FOR RESIDUE NAP C 1002
3
AC3
SOFTWARE
GLY B:22 , THR B:23 , TYR B:24 , ASP B:50 , TYR B:55 , HIS B:117 , SER B:166 , ASN B:167 , GLN B:190 , HIS B:216 , SER B:217 , ALA B:218 , LEU B:219 , GLY B:220 , THR B:221 , GLN B:222 , ALA B:253 , LEU B:268 , LYS B:270 , SER B:271 , TYR B:272 , ASN B:273 , ARG B:276 , GLU B:279 , ASN B:280 , HOH B:1133 , HOH B:1142
BINDING SITE FOR RESIDUE NAP B 1003
[
close Site info
]
SAPs(SNPs)/Variants
(5, 15)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_028240 (G135E, chain A/B/C, )
2: VAR_013290 (S145C, chain A/B/C, )
3: VAR_028241 (Y170Y, chain A/B/C, )
4: VAR_028242 (R250R, chain A/B/C, )
5: VAR_013291 (L311V, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_028240
G
135
E
AK1C4_HUMAN
Polymorphism
11253043
A/B/C
G
135
E
2
UniProt
VAR_013290
S
145
C
AK1C4_HUMAN
Polymorphism
3829125
A/B/C
S
145
C
3
UniProt
VAR_028241
C
170
Y
AK1C4_HUMAN
Polymorphism
17851824
A/B/C
Y
170
Y
4
UniProt
VAR_028242
Q
250
R
AK1C4_HUMAN
Polymorphism
4880718
A/B/C
R
250
R
5
UniProt
VAR_013291
L
311
V
AK1C4_HUMAN
Polymorphism
17134592
A/B/C
L
311
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 9)
Info
All PROSITE Patterns/Profiles
1: ALDOKETO_REDUCTASE_1 (A:45-62,B:45-62,C:45-62)
2: ALDOKETO_REDUCTASE_2 (A:151-168,B:151-168,C:151-168)
3: ALDOKETO_REDUCTASE_3 (A:268-283,B:268-283,C:268-283)
;
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.
AK1C4_HUMAN
45-62
3
A:45-62
B:45-62
C:45-62
2
ALDOKETO_REDUCTASE_2
PS00062
Aldo/keto reductase family signature 2.
AK1C4_HUMAN
151-168
3
A:151-168
B:151-168
C:151-168
3
ALDOKETO_REDUCTASE_3
PS00063
Aldo/keto reductase family putative active site signature.
AK1C4_HUMAN
268-283
3
A:268-283
B:268-283
C:268-283
[
close PROSITE info
]
Exons
(9, 27)
Info
All Exons
Exon 1.2c (A:1-28 | B:1-28 | C:1-28)
Exon 1.3 (A:29-84 | B:29-84 | C:29-84)
Exon 1.4 (A:85-123 | B:85-123 | C:85-123)
Exon 1.6 (A:124-149 | B:124-149 | C:124-149)
Exon 1.7 (A:150-190 | B:150-190 | C:150-190)
Exon 1.8 (A:191-227 | B:191-227 | C:191-227)
Exon 1.9 (A:227-282 | B:227-282 | C:227-282)
Exon 1.10 (A:283-310 | B:283-310 | C:283-310)
Exon 1.11 (A:310-323 | B:310-323 | C:310-323)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.2a/1.2c
02: Boundary 1.2c/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.6
05: Boundary 1.6/1.7
06: Boundary 1.7/1.8
07: Boundary 1.8/1.9
08: Boundary 1.9/1.10
09: Boundary 1.10/1.11
10: Boundary 1.11/-
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
1.1
ENST00000380448
1
ENSE00001485164
chr10:
5237426-5237538
113
AK1C4_HUMAN
-
0
0
-
-
1.2a
ENST00000380448
2a
ENSE00001485161
chr10:
5238192-5238283
92
AK1C4_HUMAN
-
0
0
-
-
1.2c
ENST00000380448
2c
ENSE00001485159
chr10:
5238783-5238914
132
AK1C4_HUMAN
1-28
28
3
A:1-28
B:1-28
C:1-28
28
28
28
1.3
ENST00000380448
3
ENSE00001791891
chr10:
5242144-5242311
168
AK1C4_HUMAN
29-84
56
3
A:29-84
B:29-84
C:29-84
56
56
56
1.4
ENST00000380448
4
ENSE00001702720
chr10:
5246340-5246456
117
AK1C4_HUMAN
85-123
39
3
A:85-123
B:85-123
C:85-123
39
39
39
1.6
ENST00000380448
6
ENSE00000688888
chr10:
5247720-5247797
78
AK1C4_HUMAN
124-149
26
3
A:124-149
B:124-149
C:124-149
26
26
26
1.7
ENST00000380448
7
ENSE00001677400
chr10:
5248238-5248360
123
AK1C4_HUMAN
150-190
41
3
A:150-190
B:150-190
C:150-190
41
41
41
1.8
ENST00000380448
8
ENSE00001800428
chr10:
5254579-5254688
110
AK1C4_HUMAN
191-227
37
3
A:191-227
B:191-227
C:191-227
37
37
37
1.9
ENST00000380448
9
ENSE00001628752
chr10:
5254957-5255122
166
AK1C4_HUMAN
227-282
56
3
A:227-282
B:227-282
C:227-282
56
56
56
1.10
ENST00000380448
10
ENSE00001336293
chr10:
5258674-5258756
83
AK1C4_HUMAN
283-310
28
3
A:283-310
B:283-310
C:283-310
28
28
28
1.11
ENST00000380448
11
ENSE00001132424
chr10:
5260681-5260912
232
AK1C4_HUMAN
310-323
14
3
A:310-323
B:310-323
C:310-323
14
14
14
[
close EXON info
]
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d2fvla_ (A:)
1b: SCOP_d2fvlb_ (B:)
1c: SCOP_d2fvlc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
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
:
automated matches
(62)
Human (Homo sapiens) [TaxId: 9606]
(48)
1a
d2fvla_
A:
1b
d2fvlb_
B:
1c
d2fvlc_
C:
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_2fvlA00 (A:1-323)
1b: CATH_2fvlB00 (B:1-323)
1c: CATH_2fvlC00 (C:1-323)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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
2fvlA00
A:1-323
1b
2fvlB00
B:1-323
1c
2fvlC00
C:1-323
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
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)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (185 KB)
Header - Asym.Unit
Biol.Unit 1 (62 KB)
Header - Biol.Unit 1
Biol.Unit 2 (61 KB)
Header - Biol.Unit 2
Biol.Unit 3 (62 KB)
Header - Biol.Unit 3
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2FVL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help