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.
2USH
Biol. Unit 2
Info
Asym.Unit (174 KB)
Biol.Unit 1 (85 KB)
Biol.Unit 2 (87 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
5'-NUCLEOTIDASE FROM E. COLI
Authors
:
T. Knofel, N. Strater
Date
:
24 Sep 98 (Deposition) - 15 Jun 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.22
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
5'-Nucleotidase, Udp-Sugar Hydrolase, Phosphatase, Hydrolase (Phosphoric Monoester), Periplasmic Protein, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Knofel, N. Strater
X-Ray Structure Of The Escherichia Coli Periplasmic 5'-Nucleotidase Containing A Dimetal Catalytic Site.
Nat. Struct. Biol. V. 6 448 1999
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: TUNGSTATE(VI)ION (WO4a)
1b: TUNGSTATE(VI)ION (WO4b)
1c: TUNGSTATE(VI)ION (WO4c)
1d: TUNGSTATE(VI)ION (WO4d)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
2i: ZINC ION (ZNi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
WO4
2
Ligand/Ion
TUNGSTATE(VI)ION
2
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(11, 11)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC2 (SOFTWARE)
10: BC3 (SOFTWARE)
11: ZNB (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
ASP B:41 , HIS B:43 , ASP B:84 , GLN B:254 , ZN B:602 , HOH B:880
BINDING SITE FOR RESIDUE ZN B 601
02
AC4
SOFTWARE
ASP B:41 , ASP B:84 , ASN B:116 , HIS B:217 , HIS B:252 , ZN B:601 , HOH B:880
BINDING SITE FOR RESIDUE ZN B 602
03
AC5
SOFTWARE
WO4 A:702 , LYS B:322 , WO4 B:704
BINDING SITE FOR RESIDUE WO4 B 701
04
AC6
SOFTWARE
ARG A:375 , WO4 A:703 , ARG B:410 , WO4 B:701 , WO4 B:704
BINDING SITE FOR RESIDUE WO4 A 702
05
AC7
SOFTWARE
ARG A:375 , ARG A:379 , ARG A:410 , WO4 A:702 , ZN A:709 , ARG B:375 , WO4 B:704
BINDING SITE FOR RESIDUE WO4 A 703
06
AC8
SOFTWARE
WO4 A:702 , WO4 A:703 , ARG B:410 , WO4 B:701
BINDING SITE FOR RESIDUE WO4 B 704
07
AC9
SOFTWARE
ASP A:194 , HIS B:226 , GLU B:235
BINDING SITE FOR RESIDUE ZN B 705
08
BC1
SOFTWARE
HIS A:226 , GLU A:235 , GLU B:225
BINDING SITE FOR RESIDUE ZN B 706
09
BC2
SOFTWARE
ASP A:374 , ASP A:376 , ASP B:29 , ASP B:376
BINDING SITE FOR RESIDUE ZN A 707
10
BC3
SOFTWARE
HIS A:289 , GLU A:290 , LYS A:293 , GLU B:326
BINDING SITE FOR RESIDUE ZN A 708
11
ZNB
UNKNOWN
ASP B:41 , HIS B:43 , ASP B:84 , ASN B:116 , HIS B:217 , HIS B:252 , GLN B:254
ZN BINDING SITE
[
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
(2, 2)
Info
All PROSITE Patterns/Profiles
1: 5_NUCLEOTIDASE_1 (B:34-46)
2: 5_NUCLEOTIDASE_2 (B:109-120)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
5_NUCLEOTIDASE_1
PS00785
5'-nucleotidase signature 1.
USHA_ECOLI
34-46
1
-
B:34-46
2
5_NUCLEOTIDASE_2
PS00786
5'-nucleotidase signature 2.
USHA_ECOLI
109-120
1
-
B:109-120
[
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2usha1 (A:363-549)
1b: SCOP_d2ushb1 (B:363-549)
2a: SCOP_d2usha2 (A:26-362)
2b: SCOP_d2ushb2 (B:26-362)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
(10)
Superfamily
:
5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
(10)
Family
:
5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
(10)
Protein domain
:
5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
(10)
Escherichia coli [TaxId: 562]
(8)
1a
d2usha1
A:363-549
1b
d2ushb1
B:363-549
Fold
:
Metallo-dependent phosphatases
(115)
Superfamily
:
Metallo-dependent phosphatases
(115)
Family
:
5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain
(10)
Protein domain
:
5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain
(10)
Escherichia coli [TaxId: 562]
(8)
2a
d2usha2
A:26-362
2b
d2ushb2
B:26-362
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2ushA01 (A:26-362)
1b: CATH_2ushB01 (B:26-362)
2a: CATH_2ushB02 (B:363-548)
2b: CATH_2ushA02 (A:363-546)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Purple Acid Phosphatase; chain A, domain 2
(87)
Homologous Superfamily
:
[code=3.60.21.10, no name defined]
(83)
Escherichia coli k12. Organism_taxid: 83333. Strain: k12.
(2)
1a
2ushA01
A:26-362
1b
2ushB01
B:26-362
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
5'-nucleotidase; domain 2
(9)
Homologous Superfamily
:
5'-nucleotidase; Domain 2
(9)
Escherichia coli k12. Organism_taxid: 83333. Strain: k12.
(2)
2a
2ushB02
B:363-548
2b
2ushA02
A:363-546
[
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 B
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 (174 KB)
Header - Asym.Unit
Biol.Unit 1 (85 KB)
Header - Biol.Unit 1
Biol.Unit 2 (87 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
2USH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
