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.
2V7G
Biol. Unit 4
Info
Asym.Unit (373 KB)
Biol.Unit 1 (366 KB)
Biol.Unit 2 (365 KB)
Biol.Unit 3 (186 KB)
Biol.Unit 4 (185 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 AN ENGINEERED UROCANASE TETRAMER
Authors
:
N. Treiber, G. E. Schulz
Date
:
30 Jul 07 (Deposition) - 15 Jan 08 (Release) - 20 Nov 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B,C,D (1x)
Biol. Unit 3: A,C (1x)
Biol. Unit 4: B,D (1x)
Keywords
:
Histidine Degradation, Nad, Lyase, Protein Engineering, Urocanate Hydratase, Histidine Metabolism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Grueninger, N. Treiber, M. O. P. Ziegler, J. W. A. Koetter, M. -S. Schulze, G. E. Schulz
Designed Protein-Protein Association.
Science V. 319 206 2008
[
close entry info
]
Hetero Components
(3, 12)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
3a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
3b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
3d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
3
Ligand/Ion
ACETATE ION
2
GOL
7
Ligand/Ion
GLYCEROL
3
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC3 (SOFTWARE)
07: BC4 (SOFTWARE)
08: BC5 (SOFTWARE)
09: BC6 (SOFTWARE)
10: BC7 (SOFTWARE)
11: BC8 (SOFTWARE)
12: BC9 (SOFTWARE)
13: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
GLU B:44 , TYR B:52 , GLY B:53 , GLY B:54 , GLN B:131 , ILE B:145 , GLY B:176 , GLY B:177 , MET B:178 , GLY B:179 , GLU B:197 , SER B:198 , GLN B:199 , ARG B:202 , GLY B:242 , ASN B:243 , ALA B:244 , GLN B:264 , THR B:265 , SER B:266 , HIS B:268 , GLY B:273 , TYR B:274 , LEU B:275 , TRP B:281 , TYR B:323 , GLY B:324 , ASN B:325 , PHE B:345 , LEU B:445 , ARG B:455 , GLY B:493 , HOH B:2035 , HOH B:2192 , HOH B:2340 , HOH B:2341
BINDING SITE FOR RESIDUE NAD B3001
02
AC4
SOFTWARE
GLY D:176 , GLY D:177 , MET D:178 , GLY D:179 , GLU D:197 , SER D:198 , GLN D:199 , ARG D:202 , GLY D:242 , ASN D:243 , ALA D:244 , GLN D:264 , THR D:265 , SER D:266 , HIS D:268 , GLY D:273 , TYR D:274 , LEU D:275 , TYR D:323 , GLY D:324 , ASN D:325 , PHE D:345 , ARG D:455 , HOH D:2241 , HOH D:2287 , HOH D:2288 , HOH D:2289 , HOH D:2290 , HOH D:2291 , HOH D:2292
BINDING SITE FOR RESIDUE NAD D3001
03
AC6
SOFTWARE
LYS B:87 , HOH B:2332 , HOH B:2333 , ASP D:535 , MET D:554 , ILE D:555
BINDING SITE FOR RESIDUE ACT B1558
04
AC7
SOFTWARE
VAL B:91 , HOH B:2334 , HOH B:2335 , ASP D:551
BINDING SITE FOR RESIDUE ACT B1559
05
AC9
SOFTWARE
TYR B:52 , THR B:133 , TYR B:139 , GLY B:144 , ILE B:145 , MET B:178 , ARG B:362 , ASP B:443 , HOH B:2275 , HOH B:2336
BINDING SITE FOR RESIDUE ACT B1560
06
BC3
SOFTWARE
PRO B:453 , ASN B:454 , ASP B:465 , HOH B:2220
BINDING SITE FOR RESIDUE GOL B1561
07
BC4
SOFTWARE
SER D:198 , GLY D:242 , ASN D:243 , LEU D:275 , THR D:280 , TRP D:281
BINDING SITE FOR RESIDUE GOL D1558
08
BC5
SOFTWARE
GLU B:151 , ARG B:158 , HIS B:389 , HOH B:2337 , HOH B:2338
BINDING SITE FOR RESIDUE GOL B1562
09
BC6
SOFTWARE
HOH A:2202 , GLU D:246 , GLY D:278
BINDING SITE FOR RESIDUE GOL D1559
10
BC7
SOFTWARE
ILE A:277 , TRP A:279 , ALA A:298 , SER A:302 , PRO D:276 , ILE D:277 , TRP D:279 , SER D:302
BINDING SITE FOR RESIDUE GOL A1560
11
BC8
SOFTWARE
SER D:198 , GLN D:200 , SER D:201 , HIS D:241
BINDING SITE FOR RESIDUE GOL D1560
12
BC9
SOFTWARE
HIS B:160 , GLN B:314 , THR B:320 , PRO B:343 , TYR B:349 , HOH B:2339
BINDING SITE FOR RESIDUE GOL B1563
13
CC2
SOFTWARE
GLU D:151 , ARG D:158 , LEU D:390 , TRP D:412
BINDING SITE FOR RESIDUE GOL D1561
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: UROCANASE (B:442-457,D:442-457)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UROCANASE
PS01233
Urocanase signature.
HUTU_PSEPU
442-457
2
-
B:442-457
-
D:442-457
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d2v7ga_ (A:)
1b: SCOP_d2v7gb_ (B:)
1c: SCOP_d2v7gc_ (C:)
1d: SCOP_d2v7gd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Urocanase
(6)
Superfamily
:
Urocanase
(6)
Family
:
Urocanase
(6)
Protein domain
:
automated matches
(2)
Pseudomonas putida [TaxId: 303]
(1)
1a
d2v7ga_
A:
1b
d2v7gb_
B:
1c
d2v7gc_
C:
1d
d2v7gd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2v7gA02 (A:142-349)
1b: CATH_2v7gB02 (B:142-349)
1c: CATH_2v7gC02 (C:142-349)
1d: CATH_2v7gD02 (D:142-349)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Urocanase like domains
(6)
Pseudomonas putida. Organism_taxid: 303.
(4)
1a
2v7gA02
A:142-349
1b
2v7gB02
B:142-349
1c
2v7gC02
C:142-349
1d
2v7gD02
D:142-349
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Urocanase_2v7gD01 (D:11-556)
1b: PFAM_Urocanase_2v7gD02 (D:11-556)
1c: PFAM_Urocanase_2v7gD03 (D:11-556)
1d: PFAM_Urocanase_2v7gD04 (D:11-556)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Urocanase]
(5)
Family
:
Urocanase
(5)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(4)
1a
Urocanase-2v7gD01
D:11-556
1b
Urocanase-2v7gD02
D:11-556
1c
Urocanase-2v7gD03
D:11-556
1d
Urocanase-2v7gD04
D:11-556
[
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
Chain D
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 (373 KB)
Header - Asym.Unit
Biol.Unit 1 (366 KB)
Header - Biol.Unit 1
Biol.Unit 2 (365 KB)
Header - Biol.Unit 2
Biol.Unit 3 (186 KB)
Header - Biol.Unit 3
Biol.Unit 4 (185 KB)
Header - Biol.Unit 4
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
2V7G
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
