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.
2XJA
Biol. Unit 1
Info
Asym.Unit (630 KB)
Biol.Unit 1 (160 KB)
Biol.Unit 2 (161 KB)
Biol.Unit 3 (161 KB)
Biol.Unit 4 (157 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF MURE FROM M.TUBERCULOSIS WITH DIPEPTIDE AND ADP
Authors
:
C. Basavannacharya, P. R. Moody, S. Bhakta, N. Keep
Date
:
03 Jul 10 (Deposition) - 18 Aug 10 (Release) - 29 Dec 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Ligase, Peptidoglycan, Peptidase Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Basavannacharya, P. R. Moody, T. Munshi, N. Cronin, N. H. Keep, S. Bhakta
Essential Residues For The Enzyme Activity Of Atp-Dependent Mure Ligase From Mycobacterium Tuberculosis.
Protein Cell V. 1 1011 2010
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 3)
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: LYSINE NZ-CARBOXYLIC ACID (KCXa)
2b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
2c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
2d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
4a: URIDINE-5'-DIPHOSPHATE-N-ACETYLMUR... (UAGa)
4b: URIDINE-5'-DIPHOSPHATE-N-ACETYLMUR... (UAGb)
4c: URIDINE-5'-DIPHOSPHATE-N-ACETYLMUR... (UAGc)
4d: URIDINE-5'-DIPHOSPHATE-N-ACETYLMUR... (UAGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
1
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
KCX
1
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
UAG
1
Ligand/Ion
URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:154 , SER A:155 , GLY A:156 , LYS A:157 , THR A:158 , THR A:159 , GLU A:220 , ASN A:243 , TYR A:343 , ASN A:347 , ARG A:377 , LEU A:378 , ASP A:392 , ALA A:394 , SER A:402 , MG A:1534
BINDING SITE FOR RESIDUE ADP A1533
2
AC2
SOFTWARE
THR A:158 , THR A:180 , GLU A:220 , ADP A:1533 , HOH A:2001
BINDING SITE FOR RESIDUE MG A1534
3
AC3
SOFTWARE
ASP A:247 , HIS A:248 , KCX A:262 , UAG A:1536
BINDING SITE FOR RESIDUE MG A1535
4
AC4
SOFTWARE
LEU A:67 , ARG A:68 , ALA A:69 , GLN A:70 , GLY A:83 , SER A:84 , THR A:85 , THR A:86 , GLY A:88 , HIS A:91 , ARG A:128 , LEU A:194 , THR A:195 , THR A:196 , GLU A:198 , SER A:222 , LEU A:228 , ARG A:230 , HIS A:248 , MG A:1535 , HOH A:2001
BINDING SITE FOR RESIDUE UAG A1536
[
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, 4)
Info
all CATH domains
1a: CATH_2xjaA02 (A:142-375)
1b: CATH_2xjaB02 (B:142-375)
1c: CATH_2xjaC02 (C:142-375)
1d: CATH_2xjaD02 (D:142-375)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
(109)
Homologous Superfamily
:
[code=3.40.1190.10, no name defined]
(36)
Tb (Mycobacterium tuberculosis)
(1)
1a
2xjaA02
A:142-375
1b
2xjaB02
B:142-375
1c
2xjaC02
C:142-375
1d
2xjaD02
D:142-375
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_Mur_ligase_2xjaD01 (D:61-139)
1b: PFAM_Mur_ligase_2xjaD02 (D:61-139)
1c: PFAM_Mur_ligase_2xjaD03 (D:61-139)
1d: PFAM_Mur_ligase_2xjaD04 (D:61-139)
2a: PFAM_Mur_ligase_C_2xjaD05 (D:374-459)
2b: PFAM_Mur_ligase_C_2xjaD06 (D:374-459)
2c: PFAM_Mur_ligase_C_2xjaD07 (D:374-459)
2d: PFAM_Mur_ligase_C_2xjaD08 (D:374-459)
3a: PFAM_Mur_ligase_M_2xjaD09 (D:151-355)
3b: PFAM_Mur_ligase_M_2xjaD10 (D:151-355)
3c: PFAM_Mur_ligase_M_2xjaD11 (D:151-355)
3d: PFAM_Mur_ligase_M_2xjaD12 (D:151-355)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Mur_ligase
(4)
Mycobacterium tuberculosis
(2)
1a
Mur_ligase-2xjaD01
D:61-139
1b
Mur_ligase-2xjaD02
D:61-139
1c
Mur_ligase-2xjaD03
D:61-139
1d
Mur_ligase-2xjaD04
D:61-139
Clan
:
no clan defined [family: Mur_ligase_C]
(24)
Family
:
Mur_ligase_C
(24)
Mycobacterium tuberculosis
(2)
2a
Mur_ligase_C-2xjaD05
D:374-459
2b
Mur_ligase_C-2xjaD06
D:374-459
2c
Mur_ligase_C-2xjaD07
D:374-459
2d
Mur_ligase_C-2xjaD08
D:374-459
Clan
:
no clan defined [family: Mur_ligase_M]
(23)
Family
:
Mur_ligase_M
(23)
Mycobacterium tuberculosis
(2)
3a
Mur_ligase_M-2xjaD09
D:151-355
3b
Mur_ligase_M-2xjaD10
D:151-355
3c
Mur_ligase_M-2xjaD11
D:151-355
3d
Mur_ligase_M-2xjaD12
D:151-355
[
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
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 (630 KB)
Header - Asym.Unit
Biol.Unit 1 (160 KB)
Header - Biol.Unit 1
Biol.Unit 2 (161 KB)
Header - Biol.Unit 2
Biol.Unit 3 (161 KB)
Header - Biol.Unit 3
Biol.Unit 4 (157 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
2XJA
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
