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.
2R2D
Biol. Unit 2
Info
Asym.Unit (626 KB)
Biol.Unit 1 (213 KB)
Biol.Unit 10 (106 KB)
Biol.Unit 2 (214 KB)
Biol.Unit 3 (203 KB)
Biol.Unit 4 (619 KB)
Biol.Unit 5 (109 KB)
Biol.Unit 6 (103 KB)
Biol.Unit 7 (110 KB)
Biol.Unit 8 (110 KB)
Biol.Unit 9 (111 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 A QUORUM-QUENCHING LACTONASE (AIIB) FROM AGROBACTERIUM TUMEFACIENS
Authors
:
D. Liu, P. W. Thomas, J. Momb, Q. Hoang, G. A. Petsko, D. Ringe, W. Fast
Date
:
24 Aug 07 (Deposition) - 09 Oct 07 (Release) - 17 Jun 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,E (1x)
Biol. Unit 2: B,C (1x)
Biol. Unit 3: D,F (1x)
Biol. Unit 4: A,B,C,D,E,F (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: A (1x)
Biol. Unit 8: B (1x)
Biol. Unit 9: C (1x)
Biol. Unit 10: D (1x)
Keywords
:
Lactonase, N-Acyl Hompserine Lactone, Di-Nuclear Zinc Center, Quorum Quenching, Aiib, Phosphate, Agrobacterium Tumefaciens, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Liu, P. W. Thomas, J. Momb, Q. Q. Hoang, G. A. Petsko, D. Ringe, W. Fast
Structure And Specificity Of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens.
Biochemistry V. 46 11789 2007
[
close entry info
]
Hetero Components
(2, 8)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
2e: PHOSPHATE ION (PO4e)
2f: PHOSPHATE ION (PO4f)
2g: PHOSPHATE ION (PO4g)
2h: PHOSPHATE ION (PO4h)
2i: PHOSPHATE ION (PO4i)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
3i: ZINC ION (ZNi)
3j: ZINC ION (ZNj)
3k: ZINC ION (ZNk)
3l: ZINC ION (ZNl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
PO4
4
Ligand/Ion
PHOSPHATE ION
3
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC5 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC8 (SOFTWARE)
06: AC9 (SOFTWARE)
07: BC1 (SOFTWARE)
08: BC2 (SOFTWARE)
09: CC6 (SOFTWARE)
10: CC7 (SOFTWARE)
11: CC8 (SOFTWARE)
12: CC9 (SOFTWARE)
13: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
ASP B:115 , HIS B:116 , ASP B:213 , HIS B:259 , PO4 B:279
BINDING SITE FOR RESIDUE ZN B 277
02
AC5
SOFTWARE
HIS B:111 , HIS B:113 , HIS B:191 , ASP B:213 , PO4 B:279
BINDING SITE FOR RESIDUE ZN B 278
03
AC6
SOFTWARE
HIS B:111 , HIS B:113 , ASN B:114 , ASP B:115 , HIS B:116 , HIS B:191 , ASP B:213 , TYR B:216 , HIS B:259 , ZN B:277 , ZN B:278 , GOL B:281 , HOH B:350
BINDING SITE FOR RESIDUE PO4 B 279
04
AC7
SOFTWARE
HIS B:243 , GLN B:246 , TYR B:247 , ARG B:251 , HOH B:483
BINDING SITE FOR RESIDUE PO4 B 280
05
AC8
SOFTWARE
ASP C:115 , HIS C:116 , ASP C:213 , HIS C:259 , PO4 C:279
BINDING SITE FOR RESIDUE ZN C 277
06
AC9
SOFTWARE
HIS C:111 , HIS C:113 , HIS C:191 , ASP C:213 , PO4 C:279
BINDING SITE FOR RESIDUE ZN C 278
07
BC1
SOFTWARE
HIS C:111 , HIS C:113 , ASN C:114 , ASP C:115 , HIS C:116 , HIS C:191 , ASP C:213 , TYR C:216 , HIS C:259 , ZN C:277 , ZN C:278 , GOL C:281 , HOH C:319
BINDING SITE FOR RESIDUE PO4 C 279
08
BC2
SOFTWARE
GLU C:175 , ASN C:183 , HIS C:243 , GLN C:246 , TYR C:247 , SER C:250 , ARG C:251 , HOH C:314
BINDING SITE FOR RESIDUE PO4 C 280
09
CC6
SOFTWARE
HOH A:570 , MET C:1
BINDING SITE FOR RESIDUE GOL A 282
10
CC7
SOFTWARE
ILE B:41 , ASP B:115 , TYR B:216 , HIS B:259 , PO4 B:279
BINDING SITE FOR RESIDUE GOL B 281
11
CC8
SOFTWARE
ALA B:136 , ARG B:140 , HOH B:306
BINDING SITE FOR RESIDUE GOL B 282
12
CC9
SOFTWARE
ILE C:13 , ILE C:41 , ASP C:115 , TYR C:216 , HIS C:259 , PO4 C:279
BINDING SITE FOR RESIDUE GOL C 281
13
DC1
SOFTWARE
ASP B:233 , ILE B:235 , THR C:189 , ASP C:233 , GLY C:236 , HOH C:541 , HOH C:562 , HOH C:574
BINDING SITE FOR RESIDUE GOL C 282
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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 B
Chain C
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 (626 KB)
Header - Asym.Unit
Biol.Unit 1 (213 KB)
Header - Biol.Unit 1
Biol.Unit 10 (106 KB)
Header - Biol.Unit 10
Biol.Unit 2 (214 KB)
Header - Biol.Unit 2
Biol.Unit 3 (203 KB)
Header - Biol.Unit 3
Biol.Unit 4 (619 KB)
Header - Biol.Unit 4
Biol.Unit 5 (109 KB)
Header - Biol.Unit 5
Biol.Unit 6 (103 KB)
Header - Biol.Unit 6
Biol.Unit 7 (110 KB)
Header - Biol.Unit 7
Biol.Unit 8 (110 KB)
Header - Biol.Unit 8
Biol.Unit 9 (111 KB)
Header - Biol.Unit 9
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
2R2D
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
