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.
3ERP
Biol. Unit 1
Info
Asym.Unit (140 KB)
Biol.Unit 1 (524 KB)
Biol.Unit 2 (274 KB)
Biol.Unit 3 (255 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF IDP01002, A PUTATIVE OXIDOREDUCTASE FROM AND ESSENTIAL GENE OF SALMONELLA TYPHIMURIUM
Authors
:
A. U. Singer, G. Minasov, E. Evdokimova, J. S. Brunzelle, M. Kudritska, A. M. Edwards, W. F. Anderson, A. Savchenko, Center For Structural Of Infectious Diseases (Csgid)
Date
:
02 Oct 08 (Deposition) - 04 Nov 08 (Release) - 15 Feb 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.55
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (4x)
Biol. Unit 2: A (4x)
Biol. Unit 3: B (4x)
Keywords
:
Funded By The National Institute Of Allergy And Infectious Diseases Of Nih Contract Number Hhsn272200700058C, Predicted Oxidoreductase, Essential Gene, Salmonella, Molecular Replacement, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Kim, R. Flick, J. Brunzelle, A. Singer, E. Evdokimova, G. Brown, J. C. Joo, G. A. Minasov, W. F. Anderson, R. Mahadevan, A. Savchenko, A. F. Yakunin
Structural And Biochemical Studies Of Novel Aldo-Keto Reductases For The Biocatalytic Conversion Of 3-Hydroxybutanal To 1, 3-Butanediol.
Appl. Environ. Microbiol. 2017
[
close entry info
]
Hetero Components
(2, 40)
Info
All Hetero Components
1a: CACODYLATE ION (CACa)
1b: CACODYLATE ION (CACb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CAC
4
Ligand/Ion
CACODYLATE ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
EDO
36
Ligand/Ion
1,2-ETHANEDIOL
4
NA
-1
Ligand/Ion
SODIUM ION
5
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(24, 24)
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)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:155 , HIS A:159 , HOH A:765 , HOH A:767 , HOH A:770
BINDING SITE FOR RESIDUE ZN A 333
02
AC2
SOFTWARE
HIS A:138 , SER A:168 , GLN A:193 , CAC A:337
BINDING SITE FOR RESIDUE NA A 334
03
AC3
SOFTWARE
SER A:222 , LEU A:224 , GLY A:226 , HOH A:572
BINDING SITE FOR RESIDUE CL A 335
04
AC4
SOFTWARE
HIS A:155 , HIS A:159 , HOH A:575
BINDING SITE FOR RESIDUE CL A 336
05
AC5
SOFTWARE
TRP A:33 , TYR A:66 , HIS A:138 , ASN A:169 , PHE A:221 , NA A:334 , EDO A:342 , HOH A:771
BINDING SITE FOR RESIDUE CAC A 337
06
AC6
SOFTWARE
LEU A:269 , ARG A:272 , GLU A:320 , EDO A:339 , HOH A:430 , ASN B:169
BINDING SITE FOR RESIDUE EDO A 338
07
AC7
SOFTWARE
ARG A:272 , EDO A:338 , HOH A:443 , TYR B:170 , VAL B:203 , HOH B:782
BINDING SITE FOR RESIDUE EDO A 339
08
AC8
SOFTWARE
ALA A:172 , ASP A:173 , ARG A:176 , HOH A:630
BINDING SITE FOR RESIDUE EDO A 340
09
AC9
SOFTWARE
ALA A:257 , ASP A:258 , GLU A:261 , ARG A:331 , PHE A:332 , TYR B:15 , LYS B:24 , HOH B:772
BINDING SITE FOR RESIDUE EDO A 341
10
BC1
SOFTWARE
ASN A:65 , TYR A:66 , TYR A:100 , HIS A:138 , CAC A:337 , HOH A:686 , HOH A:699
BINDING SITE FOR RESIDUE EDO A 342
11
BC2
SOFTWARE
ARG A:17 , TRP A:110 , ASP A:141 , PRO A:142 , GLU A:143 , HOH A:395
BINDING SITE FOR RESIDUE EDO A 343
12
BC3
SOFTWARE
THR A:40 , ARG A:41 , HOH A:383 , ARG B:41
BINDING SITE FOR RESIDUE EDO A 344
13
BC4
SOFTWARE
CYS A:75 , ASN A:76 , ARG A:79 , HOH A:480 , ARG B:79 , HOH B:733 , HOH B:827
BINDING SITE FOR RESIDUE EDO A 345
14
BC5
SOFTWARE
ARG A:9 , GLU A:91 , TRP A:103 , ASP A:104 , HOH A:781
BINDING SITE FOR RESIDUE EDO A 346
15
BC6
SOFTWARE
HIS B:155 , HOH B:895 , HOH B:897 , HOH B:901
BINDING SITE FOR RESIDUE ZN B 333
16
BC7
SOFTWARE
LYS B:97 , HIS B:138 , SER B:168 , GLN B:193 , CAC B:338
BINDING SITE FOR RESIDUE NA B 334
17
BC8
SOFTWARE
SER B:222 , LEU B:224 , GLY B:226
BINDING SITE FOR RESIDUE CL B 335
18
BC9
SOFTWARE
SER A:317 , HOH A:430 , LYS B:195 , HOH B:665
BINDING SITE FOR RESIDUE CL B 336
19
CC1
SOFTWARE
HIS B:155 , HIS B:159 , HOH B:637
BINDING SITE FOR RESIDUE CL B 337
20
CC2
SOFTWARE
TRP B:33 , TYR B:66 , HIS B:138 , ASN B:169 , PHE B:221 , NA B:334
BINDING SITE FOR RESIDUE CAC B 338
21
CC3
SOFTWARE
ALA B:172 , ASP B:173 , ARG B:176 , HOH B:771 , HOH B:852
BINDING SITE FOR RESIDUE EDO B 339
22
CC4
SOFTWARE
ALA A:326 , TYR B:100 , THR B:101 , ARG B:139 , HOH B:550 , HOH B:577 , HOH B:638 , HOH B:693 , HOH B:884
BINDING SITE FOR RESIDUE EDO B 340
23
CC5
SOFTWARE
ARG A:41 , THR B:39 , THR B:40 , ARG B:41 , ASN B:44 , HOH B:657 , HOH B:892
BINDING SITE FOR RESIDUE EDO B 341
24
CC6
SOFTWARE
ARG A:272 , ARG A:273 , ASN A:313 , GLU B:200 , TRP B:202 , HOH B:579 , HOH B:782
BINDING SITE FOR RESIDUE EDO B 342
[
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_d3erpa_ (A:)
1b: SCOP_d3erpb_ (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)
Salmonella enterica [TaxId: 99287]
(1)
1a
d3erpa_
A:
1b
d3erpb_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
Asymmetric Unit 4
Asymmetric Unit 5
Asymmetric Unit 6
Asymmetric Unit 7
Asymmetric Unit 8
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 (140 KB)
Header - Asym.Unit
Biol.Unit 1 (524 KB)
Header - Biol.Unit 1
Biol.Unit 2 (274 KB)
Header - Biol.Unit 2
Biol.Unit 3 (255 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
3ERP
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help