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.
1YL6
Biol. Unit 1
Info
Asym.Unit (79 KB)
Biol.Unit 1 (145 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 DIHYDRODIPICOLINATE REDUCTASE (RV2773C) (CRYSTAL FORM B)
Authors
:
R. Janowski, G. Kefala, M. S. Weiss, Tb Structural Genomics Consort (Tbsgc)
Date
:
19 Jan 05 (Deposition) - 17 Jan 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Lysine Biosynthesis, Dihydrodipicolinate, Reductase, Nadh, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Janowski, G. Kefala, M. S. Weiss
The Structure Of Dihydrodipicolinate Reductase (Dapb) From Mycobacterium Tuberculosis In Three Crystal Forms.
Acta Crystallogr. , Sect. D V. 66 61 2010
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
VAL A:20 , ALA A:21 , ALA A:23 , LEU A:26
BINDING SITE FOR RESIDUE MG A 246
2
AC2
SOFTWARE
VAL B:20 , ALA B:21 , ALA B:23 , LEU B:26
BINDING SITE FOR RESIDUE MG B 246
[
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, 8)
Info
All PROSITE Patterns/Profiles
1: DAPB (A:127-144,B:127-144)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DAPB
PS01298
Dihydrodipicolinate reductase signature.
DAPB_MYCTO
127-144
4
A:127-144
B:127-144
DAPB_MYCTU
127-144
4
A:127-144
B:127-144
[
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1yl6a2 (A:106-214)
1b: SCOP_d1yl6b2 (B:106-214)
2a: SCOP_d1yl6a1 (A:2-105,A:215-245)
2b: SCOP_d1yl6b1 (B:2-105,B:215-245)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FwdE/GAPDH domain-like
(188)
Superfamily
:
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
(179)
Family
:
Dihydrodipicolinate reductase-like
(45)
Protein domain
:
Dihydrodipicolinate reductase
(11)
Mycobacterium tuberculosis [TaxId: 1773]
(5)
1a
d1yl6a2
A:106-214
1b
d1yl6b2
B:106-214
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
(179)
Protein domain
:
Dihydrodipicolinate reductase
(11)
Mycobacterium tuberculosis [TaxId: 1773]
(5)
2a
d1yl6a1
A:2-105,A:215-245
2b
d1yl6b1
B:2-105,B:215-245
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1yl6A02 (A:106-212)
1b: CATH_1yl6B02 (B:106-212)
2a: CATH_1yl6A01 (A:1-105,A:213-245)
2b: CATH_1yl6B01 (B:1-105,B:213-245)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(5)
1a
1yl6A02
A:106-212
1b
1yl6B02
B:106-212
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(22)
2a
1yl6A01
A:1-105,A:213-245
2b
1yl6B01
B:1-105,B:213-245
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_DapB_N_1yl6B01 (B:2-105)
1b: PFAM_DapB_N_1yl6B02 (B:2-105)
2a: PFAM_DapB_C_1yl6B03 (B:108-242)
2b: PFAM_DapB_C_1yl6B04 (B:108-242)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
DapB_N
(5)
Mycobacterium tuberculosis
(4)
1a
DapB_N-1yl6B01
B:2-105
1b
DapB_N-1yl6B02
B:2-105
Clan
:
no clan defined [family: DapB_C]
(5)
Family
:
DapB_C
(5)
Mycobacterium tuberculosis
(4)
2a
DapB_C-1yl6B03
B:108-242
2b
DapB_C-1yl6B04
B:108-242
[
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
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 (79 KB)
Header - Asym.Unit
Biol.Unit 1 (145 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
1YL6
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help