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.
3SE5
Asym. Unit
Info
Asym.Unit (121 KB)
Biol.Unit 1 (115 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
FIC PROTEIN FROM NEISSERIA MENINGITIDIS MUTANT DELTA8 IN COMPLEX WITH AMPPNP
Authors
:
A. Goepfert, F. Stanger, T. Schirmer
Date
:
10 Jun 11 (Deposition) - 25 Jan 12 (Release) - 15 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Ampylation, Adenylylation, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Engel, A. Goepfert, F. V. Stanger, A. Harms, A. Schmidt, T. Schirmer C. Dehio
Adenylylation Control By Intra- Or Intermolecular Active-Site Obstruction In Fic Proteins.
Nature V. 482 107 2012
[
close entry info
]
Hetero Components
(3, 12)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
1b: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPb)
1c: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPc)
1d: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: HEXAETHYLENE GLYCOL (P6Ga)
3b: HEXAETHYLENE GLYCOL (P6Gb)
3c: HEXAETHYLENE GLYCOL (P6Gc)
3d: HEXAETHYLENE GLYCOL (P6Gd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANP
4
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
P6G
4
Ligand/Ion
HEXAETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:67 , ASN A:104 , HIS A:107 , GLY A:112 , ASN A:113 , GLY A:114 , ARG A:115 , ARG A:118 , LYS A:140 , TYR A:143 , LEU A:144 , MET A:147 , GLU A:148 , MG A:203 , HOH A:325 , HOH A:332 , HOH A:372 , HOH A:390 , HOH A:391 , HOH A:410
BINDING SITE FOR RESIDUE ANP A 201
02
AC2
SOFTWARE
ASP A:30 , ARG A:33 , TYR A:48 , HOH A:394
BINDING SITE FOR RESIDUE P6G A 202
03
AC3
SOFTWARE
ANP A:201 , HOH A:390 , HOH A:410
BINDING SITE FOR RESIDUE MG A 203
04
AC4
SOFTWARE
LYS B:67 , PHE B:72 , ASN B:104 , HIS B:107 , GLY B:112 , ASN B:113 , GLY B:114 , ARG B:115 , ARG B:118 , LYS B:140 , TYR B:143 , LEU B:144 , MET B:147 , GLU B:148 , MG B:204 , HOH B:348 , HOH B:371 , HOH B:392 , HOH B:393 , HOH B:394
BINDING SITE FOR RESIDUE ANP B 201
05
AC5
SOFTWARE
HOH B:382 , LYS C:126 , LYS C:130 , VAL C:132 , ASP C:167
BINDING SITE FOR RESIDUE P6G B 202
06
AC6
SOFTWARE
LYS B:131 , LEU B:165 , SER C:28
BINDING SITE FOR RESIDUE P6G B 203
07
AC7
SOFTWARE
ANP B:201 , HOH B:393 , HOH B:394
BINDING SITE FOR RESIDUE MG B 204
08
AC8
SOFTWARE
LYS C:67 , ASN C:104 , HIS C:107 , GLU C:111 , GLY C:112 , ASN C:113 , GLY C:114 , ARG C:115 , ARG C:118 , LYS C:140 , TYR C:143 , LEU C:144 , MET C:147 , GLU C:148 , MG C:203 , HOH C:314 , HOH C:364 , HOH C:381 , HOH C:420
BINDING SITE FOR RESIDUE ANP C 201
09
AC9
SOFTWARE
ARG C:24 , TYR C:48 , GLY C:51 , ASP C:55 , HOH C:356 , HOH C:384
BINDING SITE FOR RESIDUE P6G C 202
10
BC1
SOFTWARE
ANP C:201 , HOH C:420 , HOH C:421
BINDING SITE FOR RESIDUE MG C 203
11
BC2
SOFTWARE
LYS D:67 , ASN D:104 , HIS D:107 , GLY D:112 , ASN D:113 , GLY D:114 , ARG D:115 , ARG D:118 , LYS D:140 , TYR D:143 , LEU D:144 , MET D:147 , GLU D:148 , MG D:202 , HOH D:360 , HOH D:373 , HOH D:385 , HOH D:399
BINDING SITE FOR RESIDUE ANP D 201
12
BC3
SOFTWARE
ANP D:201 , HOH D:377 , HOH D:399
BINDING SITE FOR RESIDUE MG D 202
[
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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: FIDO (A:37-162,B:37-162,C:37-162,D:37-16...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FIDO
PS51459
Fido domain profile.
NMFIC_NEIMB
37-162
4
A:37-162
B:37-162
C:37-162
D:37-162
[
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
(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 A
Chain B
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 (121 KB)
Header - Asym.Unit
Biol.Unit 1 (115 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
3SE5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
