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.
3NB2
Biol. Unit 2
Info
Asym.Unit (855 KB)
Biol.Unit 1 (218 KB)
Biol.Unit 2 (216 KB)
Biol.Unit 3 (218 KB)
Biol.Unit 4 (216 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 E. COLI O157:H7 EFFECTOR PROTEIN NLEL
Authors
:
D. Y. Lin, J. Chen
Date
:
02 Jun 10 (Deposition) - 27 Oct 10 (Release) - 19 Jan 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Secreted Effector Protein, Pentapeptide, Hect Domain, Hect E3 Ubiquitin Ligase, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Y. Lin, J. Diao, D. Zhou, J. Chen
Biochemical And Structural Studies Of A Hect-Like Ubiquitin Ligase From Escherichia Coli O157:H7.
J. Biol. Chem. V. 286 441 2011
[
close entry info
]
Hetero Components
(2, 7)
Info
All Hetero Components
1a: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTa)
1b: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTb)
2a: GLYCEROL (GOLa)
2aa: GLYCEROL (GOLaa)
2ab: GLYCEROL (GOLab)
2ac: GLYCEROL (GOLac)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
2t: GLYCEROL (GOLt)
2u: GLYCEROL (GOLu)
2v: GLYCEROL (GOLv)
2w: GLYCEROL (GOLw)
2x: GLYCEROL (GOLx)
2y: GLYCEROL (GOLy)
2z: GLYCEROL (GOLz)
3a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
3b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
3c: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESc)
3d: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESd)
3e: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESe)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
4m: SULFATE ION (SO4m)
4n: SULFATE ION (SO4n)
4o: SULFATE ION (SO4o)
4p: SULFATE ION (SO4p)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DTT
-1
Ligand/Ion
2,3-DIHYDROXY-1,4-DITHIOBUTANE
2
GOL
4
Ligand/Ion
GLYCEROL
3
MES
-1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(15, 15)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: CC2 (SOFTWARE)
05: CC3 (SOFTWARE)
06: CC4 (SOFTWARE)
07: CC5 (SOFTWARE)
08: CC6 (SOFTWARE)
09: CC7 (SOFTWARE)
10: CC8 (SOFTWARE)
11: EC6 (SOFTWARE)
12: EC8 (SOFTWARE)
13: FC2 (SOFTWARE)
14: FC3 (SOFTWARE)
15: FC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
PHE A:607 , GLY A:610 , ILE A:611 , HOH A:909 , SER B:511 , HOH B:938
BINDING SITE FOR RESIDUE GOL A 7
02
AC6
SOFTWARE
HIS A:552 , ASN A:564 , HOH A:906 , ASN B:564
BINDING SITE FOR RESIDUE GOL A 13
03
AC7
SOFTWARE
ASP A:613 , ILE A:614 , LEU A:615 , SER A:617 , HOH A:934 , ASP B:517 , GLY B:518 , HOH B:1130
BINDING SITE FOR RESIDUE GOL A 14
04
CC2
SOFTWARE
ASN B:356 , GLU B:449 , HOH B:802 , HOH B:1140
BINDING SITE FOR RESIDUE GOL B 3
05
CC3
SOFTWARE
TYR B:401 , GOL D:5
BINDING SITE FOR RESIDUE GOL B 6
06
CC4
SOFTWARE
SER A:511 , ASN B:606 , PHE B:607 , GLY B:610 , ILE B:611 , SER B:671 , HOH B:878
BINDING SITE FOR RESIDUE GOL B 8
07
CC5
SOFTWARE
TYR B:357 , HOH B:851 , TYR D:357 , GLU D:449 , HOH D:865
BINDING SITE FOR RESIDUE GOL B 10
08
CC6
SOFTWARE
GLY B:486 , MET B:487 , GLN B:488 , GLU B:489
BINDING SITE FOR RESIDUE SO4 B 783
09
CC7
SOFTWARE
ARG B:399 , PRO B:400 , TYR B:401 , VAL B:402
BINDING SITE FOR RESIDUE SO4 B 784
10
CC8
SOFTWARE
TYR A:532 , MET A:566 , PHE A:568 , PHE A:569 , HIS B:672
BINDING SITE FOR RESIDUE SO4 B 12
11
EC6
SOFTWARE
GOL B:6 , TYR D:401
BINDING SITE FOR RESIDUE GOL D 5
12
EC8
SOFTWARE
LYS B:766 , ARG B:782 , ASP D:434 , TYR D:459 , SER D:469 , TYR D:470
BINDING SITE FOR RESIDUE GOL D 26
13
FC2
SOFTWARE
ASP B:372 , ASP B:373 , ARG D:234 , ASN D:254 , GLU D:255
BINDING SITE FOR RESIDUE MES D 4
14
FC3
SOFTWARE
ARG B:234 , ASN B:254 , GLU B:255 , ASP D:372 , ASP D:373 , LYS D:374 , HOH D:830
BINDING SITE FOR RESIDUE MES D 783
15
FC6
SOFTWARE
HOH B:1145 , PHE D:398 , THR D:435 , TRP D:439 , HOH D:885 , HOH D:908
BINDING SITE FOR RESIDUE SO4 D 15
[
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
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 (855 KB)
Header - Asym.Unit
Biol.Unit 1 (218 KB)
Header - Biol.Unit 1
Biol.Unit 2 (216 KB)
Header - Biol.Unit 2
Biol.Unit 3 (218 KB)
Header - Biol.Unit 3
Biol.Unit 4 (216 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
3NB2
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
