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.
5A88
Asym. Unit
Info
Asym.Unit (201 KB)
Biol.Unit 1 (55 KB)
Biol.Unit 2 (51 KB)
Biol.Unit 3 (49 KB)
Biol.Unit 4 (50 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 THE RIBOFLAVIN KINASE MODULE OF FAD SYNTHETASE FROM CORYNEBACTERIUM AMMONIAGENES IN COMPLEX WITH ADP
Authors
:
B. Herguedas, M. Martinez-Julvez, J. A. Hermoso, M. Medina
Date
:
13 Jul 15 (Deposition) - 09 Dec 15 (Release) - 02 Mar 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.08
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: C (1x)
Biol. Unit 3: B (1x)
Biol. Unit 4: D (1x)
Keywords
:
Transferase, Riboflavin Kinase Domain, Atp-Binding, Nucleotide-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Herguedas, I. Lans, M. Sebastian, J. A. Hermoso, M. Martinez-Julvez, M. Medina
Structural Insights Into The Synthesis Of Fmn In Prokaryotic Organisms.
Acta Crystallogr. , Sect. D V. 71 2526 2015
[
close entry info
]
Hetero Components
(3, 14)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
CA
4
Ligand/Ion
CALCIUM ION
3
GOL
6
Ligand/Ion
GLYCEROL
[
close Hetero Component info
]
Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:193 , GLY A:196 , ALA A:197 , GLY A:198 , GLY A:201 , LYS A:202 , PRO A:207 , THR A:208 , ALA A:209 , ASN A:210 , SER A:269 , VAL A:271 , ARG A:274 , ASP A:275 , ALA A:276 , LEU A:278 , TYR A:279 , GOL A:1338 , CA A:1340 , HOH A:2009 , HOH A:2015 , HOH A:2020 , HOH A:2099
BINDING SITE FOR RESIDUE ADP A 501
02
AC2
SOFTWARE
GLY A:196 , ALA A:197 , ARG A:199 , THR A:208 , ASN A:210 , ADP A:501 , CA A:1340 , HOH A:2017
BINDING SITE FOR RESIDUE GOL A1338
03
AC3
SOFTWARE
VAL A:238 , GLY A:240 , MET A:242 , GLU A:243 , HOH A:2046 , HOH A:2047 , VAL C:238 , GLY C:240 , ASN C:241 , MET C:242 , GLU C:243
BINDING SITE FOR RESIDUE GOL A1339
04
AC4
SOFTWARE
VAL B:193 , GLY B:196 , ALA B:197 , GLY B:198 , PRO B:207 , THR B:208 , ALA B:209 , ASN B:210 , SER B:269 , VAL B:271 , ARG B:274 , ASP B:275 , ALA B:276 , LEU B:278 , TYR B:279 , GOL B:1337 , CA B:1338 , HOH B:2006 , HOH B:2008 , HOH B:2046 , HOH B:2070
BINDING SITE FOR RESIDUE ADP B 501
05
AC5
SOFTWARE
GLY B:196 , ALA B:197 , THR B:208 , ASN B:210 , GLU B:268 , ADP B:501 , CA B:1338 , HOH B:2013
BINDING SITE FOR RESIDUE GOL B1337
06
AC6
SOFTWARE
VAL C:193 , ARG C:195 , GLY C:196 , GLY C:198 , LYS C:202 , PRO C:207 , THR C:208 , ASN C:210 , SER C:269 , VAL C:271 , ARG C:274 , ASP C:275 , ALA C:276 , LEU C:278 , TYR C:279 , GOL C:1338 , CA C:1340 , HOH C:2010 , HOH C:2072
BINDING SITE FOR RESIDUE ADP C 501
07
AC7
SOFTWARE
ALA C:197 , THR C:208 , ASN C:210 , GLU C:268 , ADP C:501 , GOL C:1339 , CA C:1340
BINDING SITE FOR RESIDUE GOL C1338
08
AC8
SOFTWARE
VAL A:300 , GLY C:200 , GLY C:201 , PHE C:206 , THR C:208 , GLU C:268 , MET C:307 , GOL C:1338
BINDING SITE FOR RESIDUE GOL C1339
09
AC9
SOFTWARE
VAL D:193 , ARG D:195 , GLY D:196 , PRO D:207 , THR D:208 , ALA D:209 , ASN D:210 , SER D:269 , VAL D:271 , ARG D:274 , ASP D:275 , ALA D:276 , LEU D:278 , TYR D:279 , GOL D:1337 , CA D:1338 , HOH D:2005 , HOH D:2006 , HOH D:2052 , HOH D:2053
BINDING SITE FOR RESIDUE ADP D 501
10
BC1
SOFTWARE
GLY D:196 , THR D:208 , ASN D:210 , ADP D:501 , CA D:1338 , HOH D:2007
BINDING SITE FOR RESIDUE GOL D1337
11
BC2
SOFTWARE
THR A:208 , ASN A:210 , ADP A:501 , GOL A:1338
BINDING SITE FOR RESIDUE CA A1340
12
BC3
SOFTWARE
THR B:208 , ASN B:210 , ADP B:501 , GOL B:1337
BINDING SITE FOR RESIDUE CA B1338
13
BC4
SOFTWARE
THR C:208 , ASN C:210 , ADP C:501 , GOL C:1338
BINDING SITE FOR RESIDUE CA C1340
14
BC5
SOFTWARE
THR D:208 , ASN D:210 , ADP D:501 , GOL D:1337
BINDING SITE FOR RESIDUE CA D1338
[
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
(0, 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.
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 (201 KB)
Header - Asym.Unit
Biol.Unit 1 (55 KB)
Header - Biol.Unit 1
Biol.Unit 2 (51 KB)
Header - Biol.Unit 2
Biol.Unit 3 (49 KB)
Header - Biol.Unit 3
Biol.Unit 4 (50 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
5A88
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
