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.
1EHI
Asym. Unit
Info
Asym.Unit (124 KB)
Biol.Unit 1 (120 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
D-ALANINE:D-LACTATE LIGASE (LMDDL2) OF VANCOMYCIN-RESISTANT LEUCONOSTOC MESENTEROIDES
Authors
:
A. P. Kuzin, T. Sun, J. Jorczak-Baillass, V. L. Healy, C. T. Walsh, J. R. Knox
Date
:
21 Feb 00 (Deposition) - 23 May 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.38
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Atp-Binding. Grasp Motif For Atp. , Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. P. Kuzin, T. Sun, J. Jorczak-Baillass, V. L. Healy, C. T. Walsh, J. R. Knox
Enzymes Of Vancomycin Resistance: The Structure Of D-Alanine-D-Lactate Ligase Of Naturally Resistant Leuconostoc Mesenteroides.
Structure Fold. Des. V. 8 463 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 4)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: 1(S)-AMINOETHYL-(2-CARBOXYPROPYL)P... (PHYa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
1
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
MG
2
Ligand/Ion
MAGNESIUM ION
3
PHY
1
Ligand/Ion
1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID
[
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
GLU A:316 , ASN A:318 , ADP A:781 , PHY A:782
BINDING SITE FOR RESIDUE MG A 783
2
AC2
SOFTWARE
ASP A:303 , GLU A:316 , ADP A:781 , PHY A:782
BINDING SITE FOR RESIDUE MG A 784
3
AC3
SOFTWARE
THR A:151 , PHE A:178 , LYS A:180 , GLN A:184 , GLY A:185 , SER A:186 , SER A:187 , ILE A:190 , GLU A:216 , GLU A:217 , ALA A:218 , VAL A:219 , GLU A:224 , TRP A:254 , TYR A:255 , LYS A:260 , LEU A:305 , GLU A:316 , PHY A:782 , MG A:783 , MG A:784 , HOH A:847
BINDING SITE FOR RESIDUE ADP A 781
4
AC4
SOFTWARE
GLU A:16 , SER A:186 , LYS A:260 , PHE A:261 , ARG A:301 , ASP A:303 , GLU A:316 , ASN A:318 , GLY A:322 , MET A:326 , SER A:327 , ADP A:781 , MG A:783 , MG A:784 , HOH A:824 , HOH A:834 , HOH A:924
BINDING SITE FOR RESIDUE PHY A 782
[
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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: DALA_DALA_LIGASE_1 (A:102-113,B:502-513)
2: DALA_DALA_LIGASE_2 (A:294-322,B:694-722)
;
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_LEUMM
102-113
2
A:102-113
B:502-513
2
DALA_DALA_LIGASE_2
PS00844
D-alanine--D-alanine ligase signature 2.
DDL_LEUMM
294-322
2
A:294-322
B:694-722
[
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1ehia2 (A:135-362)
1b: SCOP_d1ehib2 (B:535-770)
2a: SCOP_d1ehia1 (A:3-134)
2b: SCOP_d1ehib1 (B:402-534)
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
:
ATP-binding domain of peptide synthetases
(9)
Protein domain
:
D-alanine:D-lactate ligase VanA, C-domain
(2)
Leuconostoc mesenteroides, Ddl2 [TaxId: 1245]
(1)
1a
d1ehia2
A:135-362
1b
d1ehib2
B:535-770
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PreATP-grasp domain
(131)
Superfamily
:
PreATP-grasp domain
(131)
Family
:
D-Alanine ligase N-terminal domain
(7)
Protein domain
:
D-alanine:D-lactate ligase VanA, N-domain
(2)
Leuconostoc mesenteroides, Ddl2 [TaxId: 1245]
(1)
2a
d1ehia1
A:3-134
2b
d1ehib1
B:402-534
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1ehiA02 (A:219-362)
1b: CATH_1ehiB02 (B:619-762)
2a: CATH_1ehiA03 (A:151-218)
2b: CATH_1ehiB03 (B:551-618)
3a: CATH_1ehiA01 (A:3-122)
3b: CATH_1ehiB01 (B:403-522)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
D-amino Acid Aminotransferase; Chain A, domain 1
(175)
Homologous Superfamily
:
ATP-grasp fold, B domain
(118)
Leuconostoc mesenteroides. Organism_taxid: 1245.
(1)
1a
1ehiA02
A:219-362
1b
1ehiB02
B:619-762
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
ATP-grasp fold, A domain
(109)
Leuconostoc mesenteroides. Organism_taxid: 1245.
(1)
2a
1ehiA03
A:151-218
2b
1ehiB03
B:551-618
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.20, no name defined]
(85)
Leuconostoc mesenteroides. Organism_taxid: 1245.
(1)
3a
1ehiA01
A:3-122
3b
1ehiB01
B:403-522
[
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
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 (124 KB)
Header - Asym.Unit
Biol.Unit 1 (120 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
1EHI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
