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.
3LMT
Biol. Unit 2
Info
Asym.Unit (161 KB)
Biol.Unit 1 (56 KB)
Biol.Unit 2 (54 KB)
Biol.Unit 3 (52 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCUTRE OF DTD FROM PLASMODIUM FALCIPARUM
Authors
:
Y. Manickam, T. K. Bhatt, S. Khan, A. Sharma
Date
:
01 Feb 10 (Deposition) - 02 Mar 10 (Release) - 27 Oct 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.75
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Dtd, Deacylase, Hydrolase, Iodide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Yogavel, S. Khan, T. K. Bhatt, A. Sharma
Structure Of D-Tyrosyl-Trnatyr Deacylase Using Home-Source Cu Kalpha And Moderate-Quality Iodide-Sad Data: Structural Polymorphism And Hepes-Bound Enzyme States
Acta Crystallogr. , Sect. D V. 66 584 2010
[
close entry info
]
Hetero Components
(1, 8)
Info
All Hetero Components
1a: IODIDE ION (IODa)
1aa: IODIDE ION (IODaa)
1ab: IODIDE ION (IODab)
1ac: IODIDE ION (IODac)
1b: IODIDE ION (IODb)
1c: IODIDE ION (IODc)
1d: IODIDE ION (IODd)
1e: IODIDE ION (IODe)
1f: IODIDE ION (IODf)
1g: IODIDE ION (IODg)
1h: IODIDE ION (IODh)
1i: IODIDE ION (IODi)
1j: IODIDE ION (IODj)
1k: IODIDE ION (IODk)
1l: IODIDE ION (IODl)
1m: IODIDE ION (IODm)
1n: IODIDE ION (IODn)
1o: IODIDE ION (IODo)
1p: IODIDE ION (IODp)
1q: IODIDE ION (IODq)
1r: IODIDE ION (IODr)
1s: IODIDE ION (IODs)
1t: IODIDE ION (IODt)
1u: IODIDE ION (IODu)
1v: IODIDE ION (IODv)
1w: IODIDE ION (IODw)
1x: IODIDE ION (IODx)
1y: IODIDE ION (IODy)
1z: IODIDE ION (IODz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IOD
8
Ligand/Ion
IODIDE ION
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: BC1 (SOFTWARE)
2: BC2 (SOFTWARE)
3: BC3 (SOFTWARE)
4: BC4 (SOFTWARE)
5: BC5 (SOFTWARE)
6: BC6 (SOFTWARE)
7: BC7 (SOFTWARE)
8: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
BC1
SOFTWARE
SER C:87 , TYR C:116 , GLY C:135 , PHE C:137
BINDING SITE FOR RESIDUE IOD C 165
2
BC2
SOFTWARE
LYS C:58 , ASN D:99
BINDING SITE FOR RESIDUE IOD C 166
3
BC3
SOFTWARE
GLN C:6 , ASN C:147 , ASN D:147
BINDING SITE FOR RESIDUE IOD C 167
4
BC4
SOFTWARE
PHE C:92
BINDING SITE FOR RESIDUE IOD C 168
5
BC5
SOFTWARE
ILE C:43
BINDING SITE FOR RESIDUE IOD C 169
6
BC6
SOFTWARE
SER D:87 , TYR D:116 , GLY D:135
BINDING SITE FOR RESIDUE IOD D 165
7
BC7
SOFTWARE
ASN D:69
BINDING SITE FOR RESIDUE IOD D 166
8
BC8
SOFTWARE
LYS D:58
BINDING SITE FOR RESIDUE IOD D 167
[
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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3lmta_ (A:)
1b: SCOP_d3lmtb_ (B:)
1c: SCOP_d3lmtc_ (C:)
1d: SCOP_d3lmtd_ (D:)
1e: SCOP_d3lmte_ (E:)
1f: SCOP_d3lmtf_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
DTD-like
(18)
Superfamily
:
DTD-like
(18)
Family
:
automated matches
(15)
Protein domain
:
automated matches
(15)
Plasmodium falciparum [TaxId: 36329]
(13)
1a
d3lmta_
A:
1b
d3lmtb_
B:
1c
d3lmtc_
C:
1d
d3lmtd_
D:
1e
d3lmte_
E:
1f
d3lmtf_
F:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Tyr_Deacylase_3lmtF01 (F:2-157)
1b: PFAM_Tyr_Deacylase_3lmtF02 (F:2-157)
1c: PFAM_Tyr_Deacylase_3lmtF03 (F:2-157)
1d: PFAM_Tyr_Deacylase_3lmtF04 (F:2-157)
1e: PFAM_Tyr_Deacylase_3lmtF05 (F:2-157)
1f: PFAM_Tyr_Deacylase_3lmtF06 (F:2-157)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Tyr_Deacylase]
(12)
Family
:
Tyr_Deacylase
(12)
Plasmodium falciparum (isolate 3D7)
(9)
1a
Tyr_Deacylase-3lmtF01
F:2-157
1b
Tyr_Deacylase-3lmtF02
F:2-157
1c
Tyr_Deacylase-3lmtF03
F:2-157
1d
Tyr_Deacylase-3lmtF04
F:2-157
1e
Tyr_Deacylase-3lmtF05
F:2-157
1f
Tyr_Deacylase-3lmtF06
F:2-157
[
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 (161 KB)
Header - Asym.Unit
Biol.Unit 1 (56 KB)
Header - Biol.Unit 1
Biol.Unit 2 (54 KB)
Header - Biol.Unit 2
Biol.Unit 3 (52 KB)
Header - Biol.Unit 3
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
3LMT
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
