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.
2F59
Biol. Unit 2
Info
Asym.Unit (124 KB)
Biol.Unit 1 (118 KB)
Biol.Unit 2 (233 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
LUMAZINE SYNTHASE RIBH1 FROM BRUCELLA ABORTUS (GENE BRUAB1_0785, SWISS-PROT ENTRY Q57DY1) COMPLEXED WITH INHIBITOR 5-NITRO-6-(D-RIBITYLAMINO)-2,4(1H,3H) PYRIMIDINEDIONE
Authors
:
S. Klinke, V. Zylberman, H. R. Bonomi, I. Haase, B. G. Guimaraes, B. C. Br A. Bacher, M. Fischer, F. A. Goldbaum
Date
:
25 Nov 05 (Deposition) - 28 Nov 06 (Release) - 16 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: A,B,C,D,E (2x)
Keywords
:
Enzyme-Substrate Analogue, Inhibitor Complex, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Klinke, V. Zylberman, H. R. Bonomi, I. Haase, B. G. Guimaraes, B. C. Braden, A. Bacher, M. Fischer, F. A. Goldbaum
Structural And Kinetic Properties Of Lumazine Synthase Isoenzymes In The Order Rhizobiales
J. Mol. Biol. V. 373 664 2007
[
close entry info
]
Hetero Components
(1, 10)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIa)
2b: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIb)
2c: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIc)
2d: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INId)
2e: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
INI
10
Mod. Residue
5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:67 , GLU A:73 , ALA E:67 , GLU E:73
BINDING SITE FOR RESIDUE CA A 301
02
AC2
SOFTWARE
GLU A:124
BINDING SITE FOR RESIDUE CA A 304
03
AC3
SOFTWARE
ALA B:67 , GLU B:73 , ALA D:67 , GLU D:73
BINDING SITE FOR RESIDUE CA B 302
04
AC4
SOFTWARE
ALA C:67 , GLU C:73
BINDING SITE FOR RESIDUE CA C 303
05
AC5
SOFTWARE
GLU C:124
BINDING SITE FOR RESIDUE CA C 305
06
AC6
SOFTWARE
ASP D:24 , ASP D:25 , ASP D:28
BINDING SITE FOR RESIDUE CA D 306
07
AC7
SOFTWARE
PHE A:22 , PRO A:51 , GLY A:52 , ALA A:53 , LEU A:54 , GLU A:55 , THR A:82 , VAL A:83 , HIS A:90 , PHE A:91 , VAL A:94 , HOH A:306 , ASN E:115 , LYS E:137 , PHE E:140
BINDING SITE FOR RESIDUE INI A 201
08
AC8
SOFTWARE
ASN A:115 , LYS A:137 , PHE A:140 , HOH A:348 , PHE B:22 , PRO B:51 , GLY B:52 , ALA B:53 , LEU B:54 , GLU B:55 , THR B:82 , VAL B:83 , HIS B:90 , PHE B:91 , VAL B:94 , HOH B:303
BINDING SITE FOR RESIDUE INI B 202
09
AC9
SOFTWARE
ASN B:115 , LYS B:137 , PHE B:140 , ALA B:144 , HOH B:331 , PHE C:22 , PRO C:51 , GLY C:52 , ALA C:53 , LEU C:54 , GLU C:55 , THR C:82 , VAL C:83 , HIS C:90 , PHE C:91 , VAL C:94 , HOH C:309
BINDING SITE FOR RESIDUE INI C 203
10
BC1
SOFTWARE
ASN C:115 , PHE C:140 , PHE D:22 , PRO D:51 , GLY D:52 , ALA D:53 , LEU D:54 , GLU D:55 , THR D:82 , VAL D:83 , HIS D:90 , PHE D:91 , VAL D:94 , HOH D:310
BINDING SITE FOR RESIDUE INI D 204
11
BC2
SOFTWARE
ASN D:115 , LYS D:137 , PHE D:140 , ALA E:20 , PHE E:22 , TYR E:23 , PRO E:51 , GLY E:52 , ALA E:53 , LEU E:54 , GLU E:55 , THR E:82 , VAL E:83 , HIS E:90 , PHE E:91 , VAL E:94 , HOH E:209
BINDING SITE FOR RESIDUE INI E 205
[
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
(1, 5)
Info
all CATH domains
1a: CATH_2f59D00 (D:11-157)
1b: CATH_2f59A00 (A:12-157)
1c: CATH_2f59B00 (B:12-157)
1d: CATH_2f59C00 (C:12-157)
1e: CATH_2f59E00 (E:12-157)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.960, no name defined]
(36)
Brucella abortus. Organism_taxid: 235.
(4)
1a
2f59D00
D:11-157
1b
2f59A00
A:12-157
1c
2f59B00
B:12-157
1d
2f59C00
C:12-157
1e
2f59E00
E:12-157
[
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
Chain E
Asymmetric Unit 1
Asymmetric Unit 2
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 (124 KB)
Header - Asym.Unit
Biol.Unit 1 (118 KB)
Header - Biol.Unit 1
Biol.Unit 2 (233 KB)
Header - Biol.Unit 2
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
2F59
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help