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.
3PET
Biol. Unit 1
Info
Asym.Unit (151 KB)
Biol.Unit 1 (145 KB)
Biol.Unit 2 (74 KB)
Biol.Unit 3 (74 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 A PUTATIVE ADHESIN (BF0245) FROM BACTEROIDES FRAGILIS NCTC 9343 AT 2.07 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
27 Oct 10 (Deposition) - 09 Feb 11 (Release) - 20 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.07
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A (1x)
Biol. Unit 3: B (1x)
Keywords
:
Right-Handed Beta-Helix, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi- Biology, Cell Adhesion
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Putative Adhesin (Bf0245) From Bacteroides Fragilis Nctc 9343 At 2. 07 A Resolution
To Be Published
[
close entry info
]
Hetero Components
(3, 20)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
4a: TETRAETHYLENE GLYCOL (PG4a)
4b: TETRAETHYLENE GLYCOL (PG4b)
4c: TETRAETHYLENE GLYCOL (PG4c)
4d: TETRAETHYLENE GLYCOL (PG4d)
4e: TETRAETHYLENE GLYCOL (PG4e)
4f: TETRAETHYLENE GLYCOL (PG4f)
4g: TETRAETHYLENE GLYCOL (PG4g)
4h: TETRAETHYLENE GLYCOL (PG4h)
4i: TETRAETHYLENE GLYCOL (PG4i)
4j: TETRAETHYLENE GLYCOL (PG4j)
4k: TETRAETHYLENE GLYCOL (PG4k)
4l: TETRAETHYLENE GLYCOL (PG4l)
4m: TETRAETHYLENE GLYCOL (PG4m)
4n: TETRAETHYLENE GLYCOL (PG4n)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
MSE
4
Mod. Amino Acid
SELENOMETHIONINE
4
PG4
14
Ligand/Ion
TETRAETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:185 , ALA A:186 , GLY A:187
BINDING SITE FOR RESIDUE CL A 246
02
AC2
SOFTWARE
VAL A:52 , ILE A:75 , ILE A:92 , PHE A:101 , MSE A:104
BINDING SITE FOR RESIDUE ACT A 247
03
AC3
SOFTWARE
TYR A:56 , TYR A:70 , LYS A:105 , HOH A:397
BINDING SITE FOR RESIDUE PG4 A 249
04
AC4
SOFTWARE
LYS A:64 , LYS A:94 , LYS A:119 , HOH A:363 , ARG B:217 , VAL B:219 , LYS B:236 , VAL B:238
BINDING SITE FOR RESIDUE PG4 A 251
05
AC5
SOFTWARE
THR A:61 , ASP A:62 , LYS A:84 , PHE A:89 , HOH A:479
BINDING SITE FOR RESIDUE PG4 A 254
06
AC6
SOFTWARE
GLU A:43 , ASN A:45 , ASN A:86 , SER A:95 , LYS A:96 , THR A:112 , HOH A:515
BINDING SITE FOR RESIDUE PG4 A 255
07
AC7
SOFTWARE
LYS A:179 , GLN A:199 , LYS B:140 , VAL B:142 , PG4 B:257
BINDING SITE FOR RESIDUE PG4 A 256
08
AC8
SOFTWARE
ALA A:171 , GLN A:172 , ARG A:190 , ASN A:192 , THR A:209
BINDING SITE FOR RESIDUE PG4 A 260
09
AC9
SOFTWARE
ASN A:128 , HOH A:549
BINDING SITE FOR RESIDUE PG4 A 261
10
BC1
SOFTWARE
ARG A:37 , THR A:61 , ILE A:79 , GLN A:80 , VAL A:81
BINDING SITE FOR RESIDUE PG4 A 262
11
BC2
SOFTWARE
GLU B:185 , ALA B:186 , GLY B:187
BINDING SITE FOR RESIDUE CL B 245
12
BC3
SOFTWARE
THR B:51 , VAL B:52 , ILE B:92 , PHE B:101 , MSE B:104
BINDING SITE FOR RESIDUE ACT B 248
13
BC4
SOFTWARE
TYR B:56 , TYR B:70 , LYS B:105
BINDING SITE FOR RESIDUE PG4 B 250
14
BC5
SOFTWARE
THR B:65 , LYS B:84 , PHE B:89
BINDING SITE FOR RESIDUE PG4 B 252
15
BC6
SOFTWARE
THR B:170 , ALA B:171 , GLN B:172 , ARG B:190 , ASN B:192 , THR B:209
BINDING SITE FOR RESIDUE PG4 B 253
16
BC7
SOFTWARE
MSE A:160 , LYS A:179 , PG4 A:256 , MSE B:160 , VAL B:162 , LYS B:179 , GLY B:180 , VAL B:181
BINDING SITE FOR RESIDUE PG4 B 257
17
BC8
SOFTWARE
GLY B:50 , LYS B:94 , LYS B:119 , PG4 B:259
BINDING SITE FOR RESIDUE PG4 B 258
18
BC9
SOFTWARE
HOH A:306 , LYS B:119 , GLY B:120 , VAL B:142 , PG4 B:258
BINDING SITE FOR RESIDUE PG4 B 259
[
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
(1, 2)
Info
all PFAM domains
1a: PFAM_DUF2807_3petB01 (B:43-228)
1b: PFAM_DUF2807_3petB02 (B:43-228)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6_Hairpin
(120)
Family
:
DUF2807
(4)
Bacteroides fragilis (strain ATCC 25285 / NCTC 9343)
(1)
1a
DUF2807-3petB01
B:43-228
1b
DUF2807-3petB02
B:43-228
[
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 (151 KB)
Header - Asym.Unit
Biol.Unit 1 (145 KB)
Header - Biol.Unit 1
Biol.Unit 2 (74 KB)
Header - Biol.Unit 2
Biol.Unit 3 (74 KB)
Header - Biol.Unit 3
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
3PET
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
