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.
2ZDH
Biol. Unit 2
Info
Asym.Unit (216 KB)
Biol.Unit 1 (108 KB)
Biol.Unit 2 (107 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 D-ALANINE:D-ALANINE LIGASE WITH ADP AND D-ALANINE FROM THERMUS THERMOPHIUS HB8
Authors
:
Y. Kitamuta, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
22 Nov 07 (Deposition) - 27 May 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
D-Alanine-D-Alanine Ligase, Peptidoglycan Biosynthesis, Cell Shape, Cell Wall Biogenesis/Degradation, Peptidoglycan Synthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Kitamura, S. Yokoyama, S. Kuramitsu
Crystal Structure Of D-Alanine:D-Alanine Ligase With Adp And D-Alanine From Thermus Thermophius Hb8
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 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: D-ALANINE (DALa)
2b: D-ALANINE (DALb)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
DAL
1
Ligand/Ion
D-ALANINE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC9 (SOFTWARE)
5: BC2 (SOFTWARE)
6: BC3 (SOFTWARE)
7: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
GLU C:282
BINDING SITE FOR RESIDUE MG C 815
2
AC6
SOFTWARE
GLU C:282
BINDING SITE FOR RESIDUE MG C 816
3
AC7
SOFTWARE
ASP D:270 , GLU D:282
BINDING SITE FOR RESIDUE MG D 817
4
AC9
SOFTWARE
LYS B:116 , PHE B:151 , LYS B:153 , SER B:159 , SER B:160 , ILE B:163 , GLU B:189 , LYS B:190 , ALA B:191 , LEU B:192 , GLU B:197 , PHE B:272 , ASN B:281 , GLU B:282 , ALA C:220
BINDING SITE FOR RESIDUE ADP B 702
5
BC2
SOFTWARE
ALA B:220 , LYS C:116 , PHE C:151 , LYS C:153 , GLY C:158 , SER C:159 , SER C:160 , ILE C:163 , GLU C:189 , LYS C:190 , ALA C:191 , LEU C:192 , GLU C:197 , PHE C:272 , ASN C:281 , GLU C:282
BINDING SITE FOR RESIDUE ADP C 703
6
BC3
SOFTWARE
LYS D:116 , PHE D:151 , LYS D:153 , GLY D:158 , SER D:159 , SER D:160 , ILE D:163 , GLU D:189 , LYS D:190 , LEU D:192 , GLU D:197 , TYR D:218 , PHE D:222 , TYR D:223 , PHE D:272 , ASN D:281 , GLU D:282
BINDING SITE FOR RESIDUE ADP D 704
7
BC4
SOFTWARE
GLU D:13 , HIS D:82 , ARG D:268 , ASN D:284 , GLY D:288
BINDING SITE FOR RESIDUE DAL D 802
[
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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: DALA_DALA_LIGASE_1 (C:82-93,D:82-93)
2: DALA_DALA_LIGASE_2 (C:261-288,D:261-288)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DALA_DALA_LIGASE_1
PS00843
D-alanine--D-alanine ligase signature 1.
DDL_THET8
82-93
2
-
-
C:82-93
D:82-93
2
DALA_DALA_LIGASE_2
PS00844
D-alanine--D-alanine ligase signature 2.
DDL_THET8
261-288
2
-
-
C:261-288
D:261-288
[
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, 8)
Info
All SCOP Domains
1a: SCOP_d2zdha2 (A:115-319)
1b: SCOP_d2zdhb2 (B:115-319)
1c: SCOP_d2zdhc2 (C:115-319)
1d: SCOP_d2zdhd2 (D:115-319)
2a: SCOP_d2zdha1 (A:1-114)
2b: SCOP_d2zdhb1 (B:1-114)
2c: SCOP_d2zdhc1 (C:1-114)
2d: SCOP_d2zdhd1 (D:1-114)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ATP-grasp
(191)
Superfamily
:
Glutathione synthetase ATP-binding domain-like
(158)
Family
:
automated matches
(42)
Protein domain
:
automated matches
(42)
Thermus thermophilus HB8 [TaxId: 300852]
(6)
1a
d2zdha2
A:115-319
1b
d2zdhb2
B:115-319
1c
d2zdhc2
C:115-319
1d
d2zdhd2
D:115-319
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PreATP-grasp domain
(131)
Superfamily
:
PreATP-grasp domain
(131)
Family
:
automated matches
(45)
Protein domain
:
automated matches
(45)
Thermus thermophilus [TaxId: 274]
(4)
2a
d2zdha1
A:1-114
2b
d2zdhb1
B:1-114
2c
d2zdhc1
C:1-114
2d
d2zdhd1
D:1-114
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Dala_Dala_lig_C_2zdhD01 (D:122-315)
1b: PFAM_Dala_Dala_lig_C_2zdhD02 (D:122-315)
1c: PFAM_Dala_Dala_lig_C_2zdhD03 (D:122-315)
1d: PFAM_Dala_Dala_lig_C_2zdhD04 (D:122-315)
2a: PFAM_Dala_Dala_lig_N_2zdhD05 (D:1-105)
2b: PFAM_Dala_Dala_lig_N_2zdhD06 (D:1-105)
2c: PFAM_Dala_Dala_lig_N_2zdhD07 (D:1-105)
2d: PFAM_Dala_Dala_lig_N_2zdhD08 (D:1-105)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ATP-grasp
(83)
Family
:
Dala_Dala_lig_C
(12)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(6)
1a
Dala_Dala_lig_C-2zdhD01
D:122-315
1b
Dala_Dala_lig_C-2zdhD02
D:122-315
1c
Dala_Dala_lig_C-2zdhD03
D:122-315
1d
Dala_Dala_lig_C-2zdhD04
D:122-315
Clan
:
no clan defined [family: Dala_Dala_lig_N]
(12)
Family
:
Dala_Dala_lig_N
(12)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(6)
2a
Dala_Dala_lig_N-2zdhD05
D:1-105
2b
Dala_Dala_lig_N-2zdhD06
D:1-105
2c
Dala_Dala_lig_N-2zdhD07
D:1-105
2d
Dala_Dala_lig_N-2zdhD08
D:1-105
[
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 C
Chain D
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 (216 KB)
Header - Asym.Unit
Biol.Unit 1 (108 KB)
Header - Biol.Unit 1
Biol.Unit 2 (107 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
2ZDH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
