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.
3DLA
Biol. Unit 1
Info
Asym.Unit (442 KB)
Biol.Unit 1 (851 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY CRYSTAL STRUCTURE OF GLUTAMINE-DEPENDENT NAD+ SYNTHETASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO NAAD+ AND DON
Authors
:
N. A. Laronde-Leblanc, M. Resto, B. Gerratana
Date
:
26 Jun 08 (Deposition) - 10 Mar 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (2x)
Keywords
:
Glutaminase, Nad+ Synthetase, Ammonia Tunneling, Enzyme, Glutamine- Dependent Nad+ Synthetase, Glutamine-Amido Transferase, Atp-Binding, Ligase, Nad, Nucleotide-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Laronde-Leblanc, M. Resto, B. Gerratana
Regulation Of Active Site Coupling In Glutamine-Dependent Nad(+) Synthetase.
Nat. Struct. Mol. Biol. V. 16 421 2009
[
close entry info
]
Hetero Components
(3, 46)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
1l: GLYCEROL (GOLl)
1m: GLYCEROL (GOLm)
1n: GLYCEROL (GOLn)
1o: GLYCEROL (GOLo)
2a: 1-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[... (NXXa)
2b: 1-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[... (NXXb)
2c: 1-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[... (NXXc)
2d: 1-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[... (NXXd)
3a: 5-OXO-L-NORLEUCINE (ONLa)
3b: 5-OXO-L-NORLEUCINE (ONLb)
3c: 5-OXO-L-NORLEUCINE (ONLc)
3d: 5-OXO-L-NORLEUCINE (ONLd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
30
Ligand/Ion
GLYCEROL
2
NXX
8
Ligand/Ion
1-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]-3-CARBOXYPYRIDINIUM
3
ONL
8
Ligand/Ion
5-OXO-L-NORLEUCINE
[
close Hetero Component info
]
Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:485 , TRP A:490 , SER A:491 , THR A:492 , TYR A:493 , ASP A:497 , PHE A:631 , PHE A:634 , LYS A:635 , SER A:661 , HOH A:811 , HOH A:937 , HOH A:1074 , HOH A:1127 , ARG D:354 , LEU D:358 , ASN D:471 , GLY D:475 , ILE D:476 , HIS D:501
BINDING SITE FOR RESIDUE NXX A 680
02
AC2
SOFTWARE
HOH A:1021 , HOH A:1128 , PRO B:125 , TYR B:127 , ARG B:128 , PHE B:130 , CYS B:176 , GLU B:177 , MET B:179 , PHE B:180 , SER B:201 , SER B:203 , ARG B:209 , ARG B:213 , TYR B:230 , MET D:286
BINDING SITE FOR RESIDUE ONL A 801
03
AC3
SOFTWARE
HOH A:1015 , LYS C:121 , PRO C:125 , TYR C:127 , PHE C:130 , CYS C:176 , GLU C:177 , PHE C:180 , ARG C:209 , HOH C:790
BINDING SITE FOR RESIDUE ONL A 802
04
AC4
SOFTWARE
HOH A:1019 , HOH A:1050 , HOH A:1082 , TYR D:127 , PHE D:130 , CYS D:176 , GLU D:177 , ARG D:209
BINDING SITE FOR RESIDUE ONL A 803
05
AC5
SOFTWARE
TYR A:127 , PHE A:130 , CYS A:176 , GLU A:177 , PHE A:180 , HOH A:1020 , HOH A:1125
BINDING SITE FOR RESIDUE ONL A 800
06
AC6
SOFTWARE
TRP B:490 , SER B:491 , THR B:492 , TYR B:493 , ASP B:497 , PHE B:631 , PHE B:634 , LYS B:635 , SER B:661 , HOH B:795 , HOH B:802 , HOH B:817 , HOH B:912 , ARG C:354 , LEU C:358 , ASN C:471 , GLY C:475 , ILE C:476 , HIS C:501 , HOH C:821
BINDING SITE FOR RESIDUE NXX B 680
07
AC7
SOFTWARE
ARG B:354 , LEU B:358 , ASN B:471 , GLY B:475 , HIS B:501 , HOH B:841 , HOH B:1007 , VAL C:452 , GLU C:455 , ASN C:456 , GLU C:485 , TRP C:490 , SER C:491 , THR C:492 , TYR C:493 , ASP C:497 , PHE C:631 , PHE C:634 , LYS C:635 , SER C:661 , HOH C:713 , HOH C:838 , HOH C:841 , HOH C:858 , HOH C:1032
BINDING SITE FOR RESIDUE NXX C 680
08
AC8
SOFTWARE
ARG A:354 , LEU A:358 , ASN A:471 , GLY A:475 , ILE A:476 , HIS A:501 , HOH A:1073 , VAL D:452 , GLU D:455 , ASN D:456 , TRP D:490 , SER D:491 , THR D:492 , TYR D:493 , ASP D:497 , PHE D:631 , PHE D:634 , LYS D:635 , SER D:661 , HOH D:759 , HOH D:827 , HOH D:828 , HOH D:845 , HOH D:911 , HOH D:978
BINDING SITE FOR RESIDUE NXX D 680
09
AC9
SOFTWARE
THR A:145 , HOH A:867 , HOH A:968
BINDING SITE FOR RESIDUE GOL A 804
10
BC1
SOFTWARE
TYR A:58 , SER A:59 , ILE A:60 , GLU A:61 , PHE A:130 , TYR A:131 , GLU A:132 , GLN A:135
BINDING SITE FOR RESIDUE GOL A 805
11
BC2
SOFTWARE
VAL B:367 , SER B:368 , PHE B:397 , ALA B:398 , LEU B:399 , HOH B:1052
BINDING SITE FOR RESIDUE GOL B 681
12
BC3
SOFTWARE
HIS B:99 , ARG B:100 , ILE B:146 , ARG B:147
BINDING SITE FOR RESIDUE GOL B 682
13
BC4
SOFTWARE
TYR A:127 , ARG A:128 , ARG A:285 , LEU A:575 , ASP A:656 , ASP B:62 , ARG B:134 , HOH B:752 , HOH B:921
BINDING SITE FOR RESIDUE GOL B 683
14
BC5
SOFTWARE
ARG B:268 , ARG B:269 , HOH B:1047
BINDING SITE FOR RESIDUE GOL B 684
15
BC6
SOFTWARE
ARG C:128 , ARG C:285 , LEU C:575 , ASP C:656 , HOH C:773 , HOH C:865 , HOH C:936 , ASP D:62 , ARG D:134
BINDING SITE FOR RESIDUE GOL C 681
16
BC7
SOFTWARE
ALA C:27 , ALA C:72 , ASP C:75 , ALA C:76 , HOH C:805
BINDING SITE FOR RESIDUE GOL C 682
17
BC8
SOFTWARE
LEU C:124 , PRO C:125 , THR C:126 , TYR C:127 , ARG C:285 , GLY C:287 , THR C:288 , ASP C:291 , ARG D:102 , ARG D:133 , ARG D:134 , HOH D:752 , HOH D:943
BINDING SITE FOR RESIDUE GOL C 683
18
BC9
SOFTWARE
TYR C:58 , SER C:59 , GLU C:61 , PHE C:130 , TYR C:131 , GLU C:132 , GLN C:135 , HOH C:1022
BINDING SITE FOR RESIDUE GOL C 684
19
CC1
SOFTWARE
ASP A:62 , LEU A:65 , ARG A:134 , HOH A:983 , HOH A:1010 , ARG D:285 , LEU D:575 , ASP D:656 , HOH D:781
BINDING SITE FOR RESIDUE GOL D 681
20
CC2
SOFTWARE
ARG A:133 , ARG A:294 , ARG B:133 , PRO B:138 , ASP D:291 , ARG D:294 , HOH D:1005
BINDING SITE FOR RESIDUE GOL D 682
21
CC3
SOFTWARE
ASP C:430 , ARG C:433 , LEU C:434 , HIS C:437 , ARG D:433 , LEU D:434 , HOH D:992 , HOH D:1006 , HOH D:1025
BINDING SITE FOR RESIDUE GOL D 683
22
CC4
SOFTWARE
TYR D:58 , SER D:59 , ILE D:60 , GLU D:61 , PHE D:130 , TYR D:131 , GLU D:132 , GLN D:135 , HOH D:855 , HOH D:1015
BINDING SITE FOR RESIDUE GOL D 684
23
CC5
SOFTWARE
ARG D:268 , ARG D:269 , HOH D:1002
BINDING SITE FOR RESIDUE GOL D 685
[
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
(1, 16)
Info
All PROSITE Patterns/Profiles
1: CN_HYDROLASE (A:12-276,B:12-276,C:12-276,D:12-27...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CN_HYDROLASE
PS50263
Carbon-nitrogen hydrolase domain profile.
NADE_MYCTO
12-276
8
A:12-276
B:12-276
C:12-276
D:12-276
NADE_MYCTU
12-276
8
A:12-276
B:12-276
C:12-276
D:12-276
[
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
(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
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 (442 KB)
Header - Asym.Unit
Biol.Unit 1 (851 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
3DLA
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
