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.
3GWC
Asym. Unit
Info
Asym.Unit (345 KB)
Biol.Unit 1 (171 KB)
Biol.Unit 2 (170 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 MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE SYNTHASE X BOUND TO FDUMP AND FAD
Authors
:
Seattle Structural Genomics Center For Infectious Disease (S
Date
:
31 Mar 09 (Deposition) - 28 Apr 09 (Release) - 22 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Thyx, Fad, Fdump, Flavoprotein, Methyltransferase, Nucleotide Biosynthesis, Transferase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
[
close entry info
]
Hetero Components
(3, 17)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
1c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
1d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
1e: FLAVIN-ADENINE DINUCLEOTIDE (FADe)
1f: FLAVIN-ADENINE DINUCLEOTIDE (FADf)
1g: FLAVIN-ADENINE DINUCLEOTIDE (FADg)
1h: FLAVIN-ADENINE DINUCLEOTIDE (FADh)
2a: GLYCEROL (GOLa)
3a: 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPH... (UFPa)
3b: 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPH... (UFPb)
3c: 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPH... (UFPc)
3d: 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPH... (UFPd)
3e: 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPH... (UFPe)
3f: 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPH... (UFPf)
3g: 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPH... (UFPg)
3h: 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPH... (UFPh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
8
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
GOL
1
Ligand/Ion
GLYCEROL
3
UFP
8
Ligand/Ion
5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
[
close Hetero Component info
]
Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:95 , HIS A:96 , ARG A:97 , HIS A:98 , HIS A:194 , ARG A:199 , HIS A:203 , HOH A:299 , HOH A:401 , HOH A:582 , HOH A:666 , HOH A:862 , CYS B:43 , SER B:71 , GLU B:74 , HIS B:98 , ASN B:188 , ARG B:190 , FAD B:259 , SER D:102 , GLN D:103 , SER D:105 , UFP D:260 , HOH D:749
BINDING SITE FOR RESIDUE FAD A 259
02
AC2
SOFTWARE
ARG A:87 , GLN A:103 , LEU A:104 , SER A:105 , GLN A:106 , ARG A:107 , ARG A:172 , HOH A:268 , HOH A:270 , HOH A:566 , HIS D:91 , GLU D:92 , ARG D:95 , ARG D:199 , FAD D:259
BINDING SITE FOR RESIDUE UFP A 260
03
AC3
SOFTWARE
CYS A:43 , SER A:71 , GLU A:74 , HIS A:98 , ASN A:188 , ARG A:190 , FAD A:259 , ARG B:95 , HIS B:96 , ARG B:97 , HIS B:98 , HIS B:194 , ARG B:199 , HIS B:203 , HOH B:297 , HOH B:425 , SER C:102 , GLN C:103 , SER C:105 , UFP C:260
BINDING SITE FOR RESIDUE FAD B 259
04
AC4
SOFTWARE
ARG B:87 , GLN B:103 , LEU B:104 , SER B:105 , GLN B:106 , ARG B:107 , TYR B:108 , ARG B:172 , HOH B:301 , HOH B:313 , HIS C:91 , GLU C:92 , ARG C:95 , ARG C:199 , FAD C:259
BINDING SITE FOR RESIDUE UFP B 260
05
AC5
SOFTWARE
SER B:102 , GLN B:103 , SER B:105 , UFP B:260 , HOH B:755 , ARG C:95 , HIS C:96 , ARG C:97 , HIS C:98 , HIS C:194 , ARG C:199 , HIS C:203 , HOH C:281 , HOH C:404 , HOH C:640 , HOH C:858 , CYS D:43 , SER D:71 , GLU D:74 , HIS D:98 , ASN D:188 , ARG D:190 , FAD D:259
BINDING SITE FOR RESIDUE FAD C 259
06
AC6
SOFTWARE
HIS B:91 , GLU B:92 , ARG B:95 , ARG B:199 , FAD B:259 , ARG C:87 , GLN C:103 , LEU C:104 , SER C:105 , GLN C:106 , ARG C:107 , TYR C:108 , ARG C:172 , HOH C:263 , HOH C:268
BINDING SITE FOR RESIDUE UFP C 260
07
AC7
SOFTWARE
ARG C:41 , SER C:46 , ASN C:51 , THR C:54 , TYR C:60 , HIS C:63
BINDING SITE FOR RESIDUE GOL C 261
08
AC8
SOFTWARE
SER A:102 , GLN A:103 , SER A:105 , UFP A:260 , CYS C:43 , SER C:71 , GLU C:74 , HIS C:98 , ASN C:188 , ARG C:190 , FAD C:259 , ARG D:95 , HIS D:96 , ARG D:97 , HIS D:98 , HIS D:194 , MET D:198 , ARG D:199 , HIS D:203 , HOH D:263 , HOH D:295 , HOH D:369 , HOH D:633
BINDING SITE FOR RESIDUE FAD D 259
09
AC9
SOFTWARE
HIS A:91 , GLU A:92 , ARG A:95 , ARG A:199 , FAD A:259 , ARG D:87 , GLN D:103 , LEU D:104 , SER D:105 , GLN D:106 , ARG D:107 , TYR D:108 , ARG D:172 , HOH D:261 , HOH D:267
BINDING SITE FOR RESIDUE UFP D 260
10
BC1
SOFTWARE
ARG E:95 , HIS E:96 , ARG E:97 , HIS E:98 , HIS E:194 , ARG E:199 , HIS E:203 , HOH E:288 , HOH E:345 , HOH E:584 , HOH E:924 , CYS F:43 , SER F:71 , GLU F:74 , HIS F:98 , ASN F:188 , ARG F:190 , FAD F:259 , SER H:102 , GLN H:103 , SER H:105 , UFP H:260 , HOH H:648
BINDING SITE FOR RESIDUE FAD E 259
11
BC2
SOFTWARE
ARG E:87 , GLN E:103 , LEU E:104 , SER E:105 , GLN E:106 , ARG E:107 , TYR E:108 , ARG E:172 , HOH E:265 , HIS H:91 , GLU H:92 , ARG H:95 , ARG H:199 , FAD H:259 , HOH H:284
BINDING SITE FOR RESIDUE UFP E 260
12
BC3
SOFTWARE
CYS E:43 , SER E:71 , GLU E:74 , HIS E:98 , ASN E:188 , ARG E:190 , FAD E:259 , ARG F:95 , HIS F:96 , ARG F:97 , HIS F:98 , HIS F:194 , ARG F:199 , HIS F:203 , HOH F:268 , HOH F:551 , HOH F:930 , SER G:102 , GLN G:103 , SER G:105 , TYR G:108 , UFP G:260
BINDING SITE FOR RESIDUE FAD F 259
13
BC4
SOFTWARE
ARG F:87 , GLN F:103 , LEU F:104 , SER F:105 , GLN F:106 , ARG F:107 , TYR F:108 , ARG F:172 , HOH F:265 , HOH F:836 , HIS G:91 , GLU G:92 , ARG G:95 , ARG G:199 , FAD G:259
BINDING SITE FOR RESIDUE UFP F 260
14
BC5
SOFTWARE
SER F:102 , GLN F:103 , SER F:105 , UFP F:260 , HOH F:853 , ARG G:95 , HIS G:96 , ARG G:97 , HIS G:98 , HIS G:194 , ARG G:199 , HIS G:203 , HOH G:273 , HOH G:641 , HOH G:656 , HOH G:928 , CYS H:43 , SER H:71 , GLU H:74 , HIS H:98 , ASN H:188 , ARG H:190 , FAD H:259
BINDING SITE FOR RESIDUE FAD G 259
15
BC6
SOFTWARE
HIS F:91 , GLU F:92 , ARG F:95 , ARG F:199 , FAD F:259 , HOH F:358 , ARG G:87 , GLN G:103 , LEU G:104 , SER G:105 , GLN G:106 , ARG G:107 , TYR G:108 , ARG G:172 , HOH G:264
BINDING SITE FOR RESIDUE UFP G 260
16
BC7
SOFTWARE
SER E:102 , GLN E:103 , SER E:105 , TYR E:108 , UFP E:260 , HOH E:486 , CYS G:43 , SER G:71 , GLU G:74 , HIS G:98 , ASN G:188 , ARG G:190 , FAD G:259 , ARG H:95 , HIS H:96 , ARG H:97 , HIS H:98 , HIS H:194 , MET H:198 , ARG H:199 , HIS H:203 , HOH H:398 , HOH H:518 , HOH H:718
BINDING SITE FOR RESIDUE FAD H 259
17
BC8
SOFTWARE
HIS E:91 , GLU E:92 , ARG E:95 , ARG E:199 , FAD E:259 , HOH E:261 , ARG H:87 , GLN H:103 , LEU H:104 , SER H:105 , GLN H:106 , ARG H:107 , TYR H:108 , ARG H:172 , HOH H:293
BINDING SITE FOR RESIDUE UFP H 260
[
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, 8)
Info
All PROSITE Patterns/Profiles
1: THYX (A:7-233,B:7-233,C:7-233,D:7-233,E:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THYX
PS51331
Flavin-dependent thymidylate synthase (thyX) domain profile.
THYX_MYCTO
7-233
8
A:7-233
B:7-233
C:7-233
D:7-233
E:7-233
F:7-233
G:7-233
H:7-233
THYX_MYCTU
7-233
8
A:7-233
B:7-233
C:7-233
D:7-233
E:7-233
F:7-233
G:7-233
H:7-233
[
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
Chain E
Chain F
Chain G
Chain H
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 (345 KB)
Header - Asym.Unit
Biol.Unit 1 (171 KB)
Header - Biol.Unit 1
Biol.Unit 2 (170 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
3GWC
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help