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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
1YNP
Biol. Unit 1
Info
Asym.Unit (225 KB)
Biol.Unit 1 (109 KB)
Biol.Unit 2 (113 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ALDO-KETO REDUCTASE AKR11C1 FROM BACILLUS HALODURANS (APO FORM)
Authors
:
T. Marquardt, D. Kostrewa, F. K. Winkler, X. D. Li
Date
:
25 Jan 05 (Deposition) - 06 Dec 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.25
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Aldo-Keto Reductase, Akr11C1, Nadph, Bacillus Halodurans, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Marquardt, D. Kostrewa, R. Balakrishnan, A. Gasperina, C. Kambach A. Podjarny, F. K. Winkler, G. K. Balendiran, X. D. Li
High-Resolution Crystal Structure Of Akr11C1 From Bacillus Halodurans: An Nadph-Dependent 4-Hydroxy-2, 3-Trans-Nonenal Reductase
J. Mol. Biol. V. 354 304 2005
[
close entry info
]
Hetero Components
(3, 10)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
2a: SODIUM ION (NAa)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
4a: SUCROSE (SUCa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
2
NA
-1
Ligand/Ion
SODIUM ION
3
SO4
8
Ligand/Ion
SULFATE ION
4
SUC
1
Ligand/Ion
SUCROSE
[
close Hetero Component info
]
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: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:217 , ARG A:219 , GLU A:222 , LYS A:288 , HOH A:334 , HOH A:367 , HOH A:467 , LYS B:3 , ASN B:43 , ASP B:70 , ILE B:71 , SO4 B:299 , HOH B:415
BINDING SITE FOR RESIDUE SUC A 298
02
AC2
SOFTWARE
GLU A:181 , HOH A:342 , LYS B:138 , GLY B:141 , ILE B:143
BINDING SITE FOR RESIDUE NA A 299
03
AC3
SOFTWARE
GLY A:197 , PRO A:198 , VAL A:199 , ALA A:200 , ARG A:201 , ALA A:255 , GLY A:256 , HOH A:325 , HOH A:352 , LYS B:85
BINDING SITE FOR RESIDUE SO4 A 300
04
AC4
SOFTWARE
LYS A:285 , ARG B:4 , GLN B:5 , HOH B:376 , HOH B:383 , HOH B:460 , HOH B:563
BINDING SITE FOR RESIDUE SO4 B 298
05
AC5
SOFTWARE
LYS A:288 , SUC A:298 , LYS B:3 , HIS B:12 , HOH B:322 , HOH B:335 , HOH B:402
BINDING SITE FOR RESIDUE SO4 B 299
06
AC6
SOFTWARE
ARG A:152 , HOH A:425 , HOH A:427 , ASN B:154 , HIS B:295 , HOH B:316 , HOH B:401 , HOH B:438
BINDING SITE FOR RESIDUE SO4 A 301
07
AC7
SOFTWARE
SER A:150 , ILE A:151 , ARG A:152 , HOH A:327 , HOH A:340 , HOH A:362 , HOH A:398 , HOH A:524
BINDING SITE FOR RESIDUE SO4 A 302
08
AC8
SOFTWARE
ILE A:123 , ASN A:154 , HIS A:295 , HOH A:324 , HOH A:554 , HOH A:555
BINDING SITE FOR RESIDUE SO4 A 303
09
AC9
SOFTWARE
LYS A:65 , ASP A:125 , PRO A:126 , ILE A:127 , ASP A:128 , ARG A:162 , HOH A:323 , HOH A:456 , HOH A:473
BINDING SITE FOR RESIDUE SO4 A 304
10
BC1
SOFTWARE
ARG A:206 , PRO A:235 , LEU A:236 , HOH A:365 , HOH A:430 , ARG B:206 , PRO B:235 , LEU B:236 , HOH B:349 , HOH B:553
BINDING SITE FOR RESIDUE SO4 B 300
11
BC2
SOFTWARE
ALA A:246 , HIS A:247 , ASP A:248 , ARG A:280 , HOH A:350 , HOH A:464 , HOH A:488
BINDING SITE FOR RESIDUE SO4 A 305
12
BC3
SOFTWARE
SER A:22 , GLN A:53
BINDING SITE FOR RESIDUE SO4 A 306
13
BC4
SOFTWARE
ARG A:219 , HOH A:329 , HOH A:354 , HOH A:358 , HOH A:466 , HOH A:569 , HOH A:570
BINDING SITE FOR RESIDUE SO4 A 307
14
BC6
SOFTWARE
VAL A:199 , GLY A:202 , SER A:205 , ARG A:207 , GLN A:262 , HOH A:400 , LYS B:85 , HOH B:413
BINDING SITE FOR RESIDUE GOL A 308
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
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_d1ynpa_ (A:)
1b: SCOP_d1ynpb_ (B:)
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
:
automated matches
(35)
Protein domain
:
automated matches
(35)
Bacillus halodurans [TaxId: 272558]
(2)
1a
d1ynpa_
A:
1b
d1ynpb_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Aldo_ket_red_1ynpB01 (B:15-288)
1b: PFAM_Aldo_ket_red_1ynpB02 (B:15-288)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Aldo_ket_red]
(94)
Family
:
Aldo_ket_red
(94)
Bacillus halodurans
(2)
1a
Aldo_ket_red-1ynpB01
B:15-288
1b
Aldo_ket_red-1ynpB02
B:15-288
[
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
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 (225 KB)
Header - Asym.Unit
Biol.Unit 1 (109 KB)
Header - Biol.Unit 1
Biol.Unit 2 (113 KB)
Header - Biol.Unit 2
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
1YNP
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help