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.
PLEASE WAIT...
Getting 'Exon' information from database.
1I0D
Asym. Unit
Info
Asym.Unit (127 KB)
Biol.Unit 1 (121 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HIGH RESOLUTION STRUCTURE OF THE ZINC/CADMIUM-CONTAINING PHOSPHOTRIESTERASE FROM PSEUDOMONAS DIMINUTA
Authors
:
H. M. Holden, M. M. Benning, F. M. Raushel, H. Shim
Date
:
29 Jan 01 (Deposition) - 04 Apr 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Pte, Zinc, Cadmium, Mixed Metals, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. M. Benning, H. Shim, F. M. Raushel, H. M. Holden
High Resolution X-Ray Structures Of Different Metal-Substituted Forms Of Phosphotriesterase From Pseudomonas Diminuta.
Biochemistry V. 40 2712 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(6, 25)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
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: FORMIC ACID (FMTa)
3b: FORMIC ACID (FMTb)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: 2-PHENYL-ETHANOL (PELa)
5b: 2-PHENYL-ETHANOL (PELb)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
2
Ligand/Ion
CADMIUM ION
2
EDO
15
Ligand/Ion
1,2-ETHANEDIOL
3
FMT
2
Ligand/Ion
FORMIC ACID
4
NA
2
Ligand/Ion
SODIUM ION
5
PEL
2
Ligand/Ion
2-PHENYL-ETHANOL
6
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(25, 25)
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)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:55 , HIS A:57 , ASP A:301 , FMT A:369 , CD A:402 , EDO A:406 , HOH A:1054
BINDING SITE FOR RESIDUE ZN A 401
02
AC2
SOFTWARE
HIS A:201 , HIS A:230 , FMT A:369 , ZN A:401 , HOH A:876 , HOH A:1054 , HOH A:1056
BINDING SITE FOR RESIDUE CD A 402
03
AC3
SOFTWARE
HIS B:55 , HIS B:57 , ASP B:301 , FMT B:369 , CD B:402 , EDO B:405 , HOH B:1053
BINDING SITE FOR RESIDUE ZN B 401
04
AC4
SOFTWARE
HIS B:201 , HIS B:230 , FMT B:369 , ZN B:401 , HOH B:1053 , HOH B:1055 , HOH B:1059
BINDING SITE FOR RESIDUE CD B 402
05
AC5
SOFTWARE
ASN A:38 , ILE A:154 , HOH A:796 , HOH A:1058 , HOH A:1063
BINDING SITE FOR RESIDUE NA A 403
06
AC6
SOFTWARE
ASN B:38 , ILE B:154 , HOH B:794 , HOH B:818 , HOH B:1062
BINDING SITE FOR RESIDUE NA B 404
07
AC7
SOFTWARE
HIS B:57 , TRP B:131 , ASP B:301 , FMT B:369 , ZN B:401 , EDO B:420 , HOH B:524 , HOH B:1053 , HOH B:1055
BINDING SITE FOR RESIDUE EDO B 405
08
AC8
SOFTWARE
HIS A:57 , ILE A:106 , TRP A:131 , FMT A:369 , ZN A:401 , EDO A:421 , HOH A:1054 , HOH A:1056
BINDING SITE FOR RESIDUE EDO A 406
09
AC9
SOFTWARE
ARG A:91 , THR B:147 , HOH B:715 , HOH B:795 , HOH B:1129
BINDING SITE FOR RESIDUE EDO B 407
10
BC1
SOFTWARE
HOH A:802 , HOH A:1057 , HOH A:1066 , HOH A:1087
BINDING SITE FOR RESIDUE EDO A 408
11
BC2
SOFTWARE
GLU A:81 , VAL A:84 , GLU A:115 , ALA A:119 , HOH A:488 , HOH A:823
BINDING SITE FOR RESIDUE EDO A 409
12
BC3
SOFTWARE
THR A:147 , ARG A:189 , EDO A:411 , HOH A:555 , HOH A:792 , HOH A:1060 , ARG B:91
BINDING SITE FOR RESIDUE EDO A 410
13
BC4
SOFTWARE
EDO A:410 , ARG B:91 , ASP B:121
BINDING SITE FOR RESIDUE EDO A 411
14
BC5
SOFTWARE
LYS B:77 , ALA B:80 , GLU B:115 , GLU B:344 , HOH B:1116
BINDING SITE FOR RESIDUE EDO B 412
15
BC6
SOFTWARE
PRO B:256 , TRP B:277 , VAL B:320 , PHE B:327 , HOH B:798
BINDING SITE FOR RESIDUE EDO B 413
16
BC7
SOFTWARE
LYS B:77 , MET B:293 , LYS B:294 , GLY B:348 , ASN B:353
BINDING SITE FOR RESIDUE PEL B 414
17
BC8
SOFTWARE
LYS A:77 , MET A:293 , THR A:345 , GLY A:348 , ILE A:349 , ASN A:353 , HOH A:890
BINDING SITE FOR RESIDUE PEL A 415
18
BC9
SOFTWARE
ASP A:133 , PRO A:134 , PRO A:135 , HOH A:459 , HOH A:460 , HOH A:462 , ASP B:133 , PRO B:134 , PRO B:135 , HOH B:521
BINDING SITE FOR RESIDUE EDO A 416
19
CC1
SOFTWARE
SER A:47 , GLU A:48 , ARG A:96
BINDING SITE FOR RESIDUE EDO A 417
20
CC2
SOFTWARE
SER B:47 , GLU B:48 , GLY B:50 , ARG B:96 , HIS B:123 , HOH B:639 , HOH B:1030
BINDING SITE FOR RESIDUE EDO B 418
21
CC3
SOFTWARE
ARG A:41 , GLY A:42 , PRO A:43 , GLU B:338 , HOH B:803
BINDING SITE FOR RESIDUE EDO A 419
22
CC4
SOFTWARE
HIS B:257 , ASP B:301 , LEU B:303 , EDO B:405 , HOH B:1053
BINDING SITE FOR RESIDUE EDO B 420
23
CC5
SOFTWARE
PHE A:306 , SER A:308 , TYR A:309 , EDO A:406
BINDING SITE FOR RESIDUE EDO A 421
24
CC6
SOFTWARE
HIS A:55 , HIS A:57 , LYS A:169 , HIS A:201 , HIS A:230 , ZN A:401 , CD A:402 , EDO A:406 , HOH A:1054
BINDING SITE FOR RESIDUE FMT A 369
25
CC7
SOFTWARE
HIS B:55 , HIS B:57 , LYS B:169 , HIS B:201 , HIS B:230 , ZN B:401 , CD B:402 , EDO B:405 , HOH B:1053
BINDING SITE FOR RESIDUE FMT B 369
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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 (A:35-363,B:35-363)
2: PHOSPHOTRIESTERASE_1 (A:50-58,B:50-58)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PHOSPHOTRIESTERASE_2
PS51347
Phosphotriesterase family profile.
OPD_BREDI
35-363
2
A:35-363
B:35-363
2
PHOSPHOTRIESTERASE_1
PS01322
Phosphotriesterase family signature 1.
OPD_BREDI
50-58
2
A:50-58
B:50-58
[
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.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1i0da_ (A:)
1b: SCOP_d1i0db_ (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
:
Metallo-dependent hydrolases
(273)
Family
:
Phosphotriesterase-like
(43)
Protein domain
:
Phosphotriesterase (parathion hydrolase, PTE)
(39)
Pseudomonas diminuta [TaxId: 293]
(19)
1a
d1i0da_
A:
1b
d1i0db_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1i0dA00 (A:35-365)
1b: CATH_1i0dB00 (B:34-364)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Brevundimonas diminuta. Organism_taxid: 293.
(6)
1a
1i0dA00
A:35-365
1b
1i0dB00
B:34-364
[
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
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 (127 KB)
Header - Asym.Unit
Biol.Unit 1 (121 KB)
Header - Biol.Unit 1
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
1I0D
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
