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.
1W19
Biol. Unit 1
Info
Asym.Unit (138 KB)
Biol.Unit 1 (246 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 FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) PROPANE 1-PHOSPHATE
Authors
:
E. Morgunova, W. Meining, B. Illarionov, I. Haase, M. Fischer, M. Cushm A. Bacher, R. Ladenstein
Date
:
18 Jun 04 (Deposition) - 02 Mar 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (2x)
Keywords
:
Transferase, Riboflavin Biosynthesis, Lumazine Synthase, Inhibitor Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Morgunova, W. Meining, B. Illarionov, I. Haase, G. Jin, A. Bacher, M. Cushman, M. Fischer, R. Ladenstein
Crystal Structure Of Lumazine Synthase From Mycobacterium Tuberculosis As A Target For Rational Drug Design: Binding Mode Of A New Class Of Purinetrione Inhibitors(, )
Biochemistry V. 44 2746 2005
[
close entry info
]
Hetero Components
(8, 32)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
1c: ACETIC ACID (ACYc)
1d: ACETIC ACID (ACYd)
1e: ACETIC ACID (ACYe)
2a: (4S,5S)-1,2-DITHIANE-4,5-DIOL (D1Da)
3a: (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-D... (DTUa)
3b: (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-D... (DTUb)
4a: (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-D... (DTVa)
4b: (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-D... (DTVb)
4c: (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-D... (DTVc)
5a: POTASSIUM ION (Ka)
5b: POTASSIUM ION (Kb)
5c: POTASSIUM ION (Kc)
5d: POTASSIUM ION (Kd)
5e: POTASSIUM ION (Ke)
5f: POTASSIUM ION (Kf)
5g: POTASSIUM ION (Kg)
5h: POTASSIUM ION (Kh)
5i: POTASSIUM ION (Ki)
5j: POTASSIUM ION (Kj)
5k: POTASSIUM ION (Kk)
5l: POTASSIUM ION (Kl)
5m: POTASSIUM ION (Km)
6a: 3-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,... (T1Pa)
7a: 3-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,... (T2Pa)
8a: 3-{2,6,8-TRIOXO-9-[(2R,3R,4R)-2,3,... (T4Pa)
8b: 3-{2,6,8-TRIOXO-9-[(2R,3R,4R)-2,3,... (T4Pb)
9a: 3-{2,6,8-TRIOXO-9-[(2S,3S,4R)-2,3,... (T5Pa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
10
Ligand/Ion
ACETIC ACID
2
D1D
2
Ligand/Ion
(4S,5S)-1,2-DITHIANE-4,5-DIOL
3
DTU
4
Ligand/Ion
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
4
DTV
6
Ligand/Ion
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
5
K
-1
Ligand/Ion
POTASSIUM ION
6
T1P
2
Ligand/Ion
3-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE
7
T2P
2
Ligand/Ion
3-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE
8
T4P
4
Ligand/Ion
3-{2,6,8-TRIOXO-9-[(2R,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE
9
T5P
2
Ligand/Ion
3-{2,6,8-TRIOXO-9-[(2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE
[
close Hetero Component info
]
Sites
(27, 27)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:70 , HIS A:73 , THR A:110 , HOH A:2033 , HOH A:2056 , HOH A:2092
BINDING SITE FOR RESIDUE K A1164
02
AC2
SOFTWARE
ALA A:34 , GLY A:38 , ALA A:129 , GLY A:130 , ASP A:137 , HOH A:2021 , HOH B:2026
BINDING SITE FOR RESIDUE K A1165
03
AC3
SOFTWARE
GLU A:155 , LEU A:156 , ARG A:157 , HIS A:159
BINDING SITE FOR RESIDUE K A1166
04
AC4
SOFTWARE
ALA B:70 , HIS B:73 , THR B:110 , HOH B:2044 , HOH B:2058 , HOH B:2086
BINDING SITE FOR RESIDUE K B1164
05
AC5
SOFTWARE
ALA B:34 , GLY B:38 , ALA B:129 , GLY B:130 , ASP B:137 , HOH B:2015 , HOH B:2017
BINDING SITE FOR RESIDUE K B1165
06
AC6
SOFTWARE
GLU B:155 , LEU B:156 , ARG B:157 , HOH B:2126 , LEU E:156 , ARG E:157 , HOH E:2127
BINDING SITE FOR RESIDUE K B1166
07
AC7
SOFTWARE
ALA C:70 , HIS C:73 , THR C:110 , HOH C:2036 , HOH C:2039 , HOH C:2067
BINDING SITE FOR RESIDUE K C1163
08
AC8
SOFTWARE
ALA C:34 , ALA C:129 , GLY C:130 , ASP C:137 , HOH C:2010 , HOH C:2091
BINDING SITE FOR RESIDUE K C1164
09
AC9
SOFTWARE
LEU C:156 , ARG C:157 , GLU D:155 , LEU D:156 , ARG D:157 , HOH D:2118
BINDING SITE FOR RESIDUE K C1165
10
BC1
SOFTWARE
ALA D:70 , HIS D:73 , THR D:110 , HOH D:2027 , HOH D:2052 , HOH D:2085
BINDING SITE FOR RESIDUE K D1164
11
BC2
SOFTWARE
ALA D:34 , ALA D:129 , GLY D:130 , ASP D:137 , HOH D:2018 , HOH D:2019
BINDING SITE FOR RESIDUE K D1165
12
BC3
SOFTWARE
ALA E:70 , HIS E:73 , THR E:110 , HOH E:2029 , HOH E:2060 , HOH E:2088
BINDING SITE FOR RESIDUE K E1164
13
BC4
SOFTWARE
ALA E:34 , ALA E:129 , GLY E:130 , ASP E:137 , HOH E:2021 , HOH E:2022
BINDING SITE FOR RESIDUE K E1165
14
BC5
SOFTWARE
ASP A:14 , CYS A:46 , ALA A:148
BINDING SITE FOR RESIDUE DTU A1162
15
BC6
SOFTWARE
TRP A:27 , HIS A:28 , ALA A:59 , ILE A:60 , GLU A:61 , VAL A:81 , VAL A:82 , ILE A:83 , GLY A:85 , GLN A:86 , THR A:87 , HIS A:89 , HOH A:2063 , HOH A:2132 , HOH A:2133 , HOH A:2134 , HOH A:2135 , HOH A:2136 , ALA B:113 , ASN B:114 , ARG B:128 , LYS B:138 , HOH B:2117
BINDING SITE FOR RESIDUE T1P A1163
16
BC7
SOFTWARE
CYS B:46 , VAL B:144 , ALA B:148
BINDING SITE FOR RESIDUE DTU B1162
17
BC8
SOFTWARE
TRP B:27 , GLY B:58 , ALA B:59 , ILE B:60 , GLU B:61 , VAL B:81 , VAL B:82 , ILE B:83 , GLY B:85 , GLN B:86 , THR B:87 , HIS B:89 , HOH B:2004 , HOH B:2066 , HOH B:2130 , HOH B:2131 , HOH B:2132 , ALA C:113 , ASN C:114 , ARG C:128 , LYS C:138 , HOH C:2090
BINDING SITE FOR RESIDUE T2P B1163
18
BC9
SOFTWARE
CYS C:46 , LEU C:151
BINDING SITE FOR RESIDUE DTV C1161
19
CC1
SOFTWARE
TRP C:27 , HIS C:28 , GLY C:58 , ALA C:59 , ILE C:60 , GLU C:61 , VAL C:81 , VAL C:82 , ILE C:83 , GLY C:85 , THR C:87 , HIS C:89 , HOH C:2043 , HOH C:2104 , HOH C:2105 , HOH C:2106 , HOH C:2107 , HOH C:2108 , ALA D:113 , ASN D:114 , ARG D:128 , LYS D:138 , HOH D:2105
BINDING SITE FOR RESIDUE T5P C1162
20
CC2
SOFTWARE
ASP D:14 , ALA D:15 , CYS D:46 , LEU D:147 , LEU D:151
BINDING SITE FOR RESIDUE DTV D1162
21
CC3
SOFTWARE
TRP D:27 , HIS D:28 , GLY D:58 , ALA D:59 , ILE D:60 , GLU D:61 , VAL D:81 , VAL D:82 , ILE D:83 , GLY D:85 , GLN D:86 , THR D:87 , HIS D:89 , HOH D:2006 , HOH D:2008 , HOH D:2057 , HOH D:2121 , HOH D:2122 , ALA E:113 , ASN E:114 , ARG E:128 , LYS E:138 , HOH E:2112
BINDING SITE FOR RESIDUE T4P D1163
22
CC4
SOFTWARE
ALA E:15 , CYS E:46 , D1D E:1166
BINDING SITE FOR RESIDUE DTV E1162
23
CC5
SOFTWARE
ALA A:113 , ASN A:114 , ARG A:128 , LYS A:138 , HOH A:2115 , TRP E:27 , HIS E:28 , ALA E:59 , ILE E:60 , GLU E:61 , VAL E:81 , VAL E:82 , ILE E:83 , GLY E:85 , GLN E:86 , THR E:87 , HIS E:89 , HOH E:2010 , HOH E:2067 , HOH E:2129 , HOH E:2130 , HOH E:2131 , HOH E:2132 , HOH E:2133
BINDING SITE FOR RESIDUE T4P E1163
24
CC6
SOFTWARE
VAL D:42 , GLY D:45 , VAL E:42 , GLY E:45 , CYS E:46 , DTV E:1162
BINDING SITE FOR RESIDUE D1D E1166
25
CC7
SOFTWARE
VAL A:56 , LEU A:57
BINDING SITE FOR RESIDUE ACY A1161
26
CC8
SOFTWARE
HOH B:2129
BINDING SITE FOR RESIDUE ACY B1161
27
CC9
SOFTWARE
ARG D:55
BINDING SITE FOR RESIDUE ACY D1161
[
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_1w19A00 (A:14-160)
1b: CATH_1w19B00 (B:14-160)
1c: CATH_1w19D00 (D:14-160)
1d: CATH_1w19C00 (C:15-160)
1e: CATH_1w19E00 (E:15-160)
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)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(8)
1a
1w19A00
A:14-160
1b
1w19B00
B:14-160
1c
1w19D00
D:14-160
1d
1w19C00
C:15-160
1e
1w19E00
E:15-160
[
close CATH info
]
Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_DMRL_synthase_1w19E01 (E:15-156)
1b: PFAM_DMRL_synthase_1w19E02 (E:15-156)
1c: PFAM_DMRL_synthase_1w19E03 (E:15-156)
1d: PFAM_DMRL_synthase_1w19E04 (E:15-156)
1e: PFAM_DMRL_synthase_1w19E05 (E:15-156)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: DMRL_synthase]
(19)
Family
:
DMRL_synthase
(19)
Mycobacterium tuberculosis
(3)
1a
DMRL_synthase-1w19E01
E:15-156
1b
DMRL_synthase-1w19E02
E:15-156
1c
DMRL_synthase-1w19E03
E:15-156
1d
DMRL_synthase-1w19E04
E:15-156
1e
DMRL_synthase-1w19E05
E:15-156
[
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 (138 KB)
Header - Asym.Unit
Biol.Unit 1 (246 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
1W19
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help