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.
2VC5
Biol. Unit 2
Info
Asym.Unit (217 KB)
Biol.Unit 1 (108 KB)
Biol.Unit 2 (107 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURAL BASIS FOR NATURAL LACTONASE AND PROMISCUOUS PHOSPHOTRIESTERASE ACTIVITIES
Authors
:
M. Elias, J. Dupuy, L. Merone, L. Mandrich, S. Moniot, C. Lecomte, M. Rossi, P. Masson, G. Manco, E. Chabriere
Date
:
18 Sep 07 (Deposition) - 15 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Phosphotriesterase, Promiscuous Activities, Enzyme Evolution, Hyperthermophilic, Lactonase, Hydrolase, Biotechnology, Quorum Sensing
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Elias, J. Dupuy, L. Merone, L. Mandrich, E. Porzio, S. Moniot, D. Rochu, C. Lecomte, M. Rossi, P. Masson, G. Manco, E. Chabriere
Structural Basis For Natural Lactonase And Promiscuous Phosphotriesterase Activities.
J. Mol. Biol. V. 379 1017 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 10)
Info
All Hetero Components
1a: COBALT (II) ION (COa)
1b: COBALT (II) ION (COb)
1c: COBALT (II) ION (COc)
1d: COBALT (II) ION (COd)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
3a: FE (III) ION (FEa)
3b: FE (III) ION (FEb)
3c: FE (III) ION (FEc)
3d: FE (III) ION (FEd)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
5a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
5b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
5c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
5d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CO
-1
Ligand/Ion
COBALT (II) ION
2
EDO
7
Ligand/Ion
1,2-ETHANEDIOL
3
FE
-1
Ligand/Ion
FE (III) ION
4
GOL
1
Ligand/Ion
GLYCEROL
5
KCX
2
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC7 (SOFTWARE)
09: CC2 (SOFTWARE)
10: CC5 (SOFTWARE)
11: CC9 (SOFTWARE)
12: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
HIS C:22 , HIS C:24 , KCX C:137 , ASP C:256 , CO C:1316 , HOH C:2056
BINDING SITE FOR RESIDUE FE C1315
02
AC6
SOFTWARE
KCX C:137 , HIS C:170 , HIS C:199 , ARG C:223 , FE C:1315 , HOH C:2013 , HOH C:2056
BINDING SITE FOR RESIDUE CO C1316
03
AC7
SOFTWARE
HIS D:22 , HIS D:24 , KCX D:137 , ASP D:256 , CO D:1316 , HOH D:2061
BINDING SITE FOR RESIDUE FE D1315
04
AC8
SOFTWARE
KCX D:137 , HIS D:170 , HIS D:199 , ARG D:223 , FE D:1315 , HOH D:2061
BINDING SITE FOR RESIDUE CO D1316
05
BC1
SOFTWARE
ASN D:172 , ALA D:173 , HIS D:174 , ASP D:202 , PHE D:229 , HOH D:2045
BINDING SITE FOR RESIDUE EDO D1317
06
BC2
SOFTWARE
ASN C:160 , LYS C:164 , GLY C:189 , ASP C:191
BINDING SITE FOR RESIDUE EDO C1317
07
BC3
SOFTWARE
PHE C:104 , TYR D:99 , ILE D:100 , ASP D:101
BINDING SITE FOR RESIDUE EDO D1318
08
BC7
SOFTWARE
ASN D:160 , LYS D:164 , GLY D:189 , VAL D:190 , ASP D:191
BINDING SITE FOR RESIDUE GOL D1319
09
CC2
SOFTWARE
GLY D:128 , THR D:129
BINDING SITE FOR RESIDUE EDO D1320
10
CC5
SOFTWARE
LEU C:39 , ILE C:261
BINDING SITE FOR RESIDUE EDO C1318
11
CC9
SOFTWARE
TYR C:99 , ILE C:100 , ASP C:101 , PHE D:104
BINDING SITE FOR RESIDUE EDO C1319
12
DC2
SOFTWARE
ALA D:266
BINDING SITE FOR RESIDUE EDO D1321
[
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, 4)
Info
All PROSITE Patterns/Profiles
1: PHOSPHOTRIESTERASE_2 (C:2-314,D:2-314)
2: PHOSPHOTRIESTERASE_1 (C:17-25,D:17-25)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PHOSPHOTRIESTERASE_2
PS51347
Phosphotriesterase family profile.
PHP_SULSO
2-314
2
-
-
C:2-314
D:2-314
2
PHOSPHOTRIESTERASE_1
PS01322
Phosphotriesterase family signature 1.
PHP_SULSO
17-25
2
-
-
C:17-25
D:17-25
[
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_d2vc5a_ (A:)
1b: SCOP_d2vc5b_ (B:)
1c: SCOP_d2vc5c_ (C:)
1d: SCOP_d2vc5d_ (D:)
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
:
Metallo-dependent hydrolases
(273)
Family
:
automated matches
(44)
Protein domain
:
automated matches
(44)
Sulfolobus solfataricus [TaxId: 2287]
(10)
1a
d2vc5a_
A:
1b
d2vc5b_
B:
1c
d2vc5c_
C:
1d
d2vc5d_
D:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_PTE_2vc5D01 (D:11-314)
1b: PFAM_PTE_2vc5D02 (D:11-314)
1c: PFAM_PTE_2vc5D03 (D:11-314)
1d: PFAM_PTE_2vc5D04 (D:11-314)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Amidohydrolase
(126)
Family
:
PTE
(19)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(2)
1a
PTE-2vc5D01
D:11-314
1b
PTE-2vc5D02
D:11-314
1c
PTE-2vc5D03
D:11-314
1d
PTE-2vc5D04
D:11-314
[
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 C
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 (217 KB)
Header - Asym.Unit
Biol.Unit 1 (108 KB)
Header - Biol.Unit 1
Biol.Unit 2 (107 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
2VC5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help