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.
2YHI
Asym. Unit
Info
Asym.Unit (175 KB)
Biol.Unit 1 (166 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
TRYPANOSOMA BRUCEI PTR1 IN COMPLEX WITH INHIBITOR WH16
Authors
:
E. Nerini, A. Dawson, W. N. Hunter, M. P. Costi
Date
:
03 May 11 (Deposition) - 23 May 12 (Release) - 23 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Short Chain Dehydrogenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Nerini, A. Dawson, V. Hannaert, P. A. Michels, W. N. Hunter, M. P. Costi
Structural Studies Of Thiadiazole Derivatives That Inhibit Trypanosoma Brucei Growth.
To Be Published
[
close entry info
]
Hetero Components
(7, 16)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
2a: S-OXY CYSTEINE (CSXa)
2b: S-OXY CYSTEINE (CSXb)
3a: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTa)
3b: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTb)
4a: (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-D... (DTUa)
5a: (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-D... (DTVa)
6a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
6b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
6c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
6d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
7a: 5-(2-CHLOROETHYL)-1,3,4-THIADIAZOL... (W16a)
7b: 5-(2-CHLOROETHYL)-1,3,4-THIADIAZOL... (W16b)
7c: 5-(2-CHLOROETHYL)-1,3,4-THIADIAZOL... (W16c)
7d: 5-(2-CHLOROETHYL)-1,3,4-THIADIAZOL... (W16d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
CSX
2
Mod. Amino Acid
S-OXY CYSTEINE
3
DTT
2
Ligand/Ion
2,3-DIHYDROXY-1,4-DITHIOBUTANE
4
DTU
1
Ligand/Ion
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
5
DTV
1
Ligand/Ion
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
6
NAP
4
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
7
W16
4
Ligand/Ion
5-(2-CHLOROETHYL)-1,3,4-THIADIAZOL-2-AMINE
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:13 , ARG A:14 , ILE A:15 , TYR A:34 , HIS A:35 , ASN A:36 , SER A:37 , ALA A:61 , ASP A:62 , LEU A:63 , THR A:64 , ASN A:93 , ALA A:94 , SER A:95 , THR A:126 , LEU A:159 , CYS A:160 , ASP A:161 , TYR A:174 , LYS A:178 , PRO A:204 , GLY A:205 , VAL A:206 , SER A:207 , LEU A:208 , W16 A:1270 , HOH A:2004 , HOH A:2005 , HOH A:2006 , HOH A:2011 , HOH A:2026 , HOH A:2064 , HOH A:2065 , HOH A:2155 , HOH A:2156
BINDING SITE FOR RESIDUE NAP A1269
02
AC2
SOFTWARE
PHE A:97 , ASP A:161 , TYR A:174 , MET A:213 , TRP A:221 , NAP A:1269 , DTV A:1271 , HOH A:2011 , HOH A:2065
BINDING SITE FOR RESIDUE W16 A1270
03
AC3
SOFTWARE
PHE A:97 , CYS A:168 , GLU A:217 , TRP A:221 , W16 A:1270 , ACT A:1272 , HOH A:2097
BINDING SITE FOR RESIDUE DTV A1271
04
AC4
SOFTWARE
PHE A:97 , DTV A:1271 , HOH A:2068
BINDING SITE FOR RESIDUE ACT A1272
05
AC5
SOFTWARE
ARG B:14 , ILE B:15 , TYR B:34 , HIS B:35 , ASN B:36 , SER B:37 , ALA B:61 , ASP B:62 , LEU B:63 , THR B:64 , ASN B:93 , ALA B:94 , SER B:95 , THR B:126 , LEU B:159 , CYS B:160 , ASP B:161 , TYR B:174 , LYS B:178 , PRO B:204 , GLY B:205 , VAL B:206 , SER B:207 , LEU B:208 , W16 B:1270 , HOH B:2005 , HOH B:2006 , HOH B:2007 , HOH B:2009 , HOH B:2013 , HOH B:2025 , HOH B:2068 , HOH B:2069 , HOH B:2151
BINDING SITE FOR RESIDUE NAP B1269
06
AC6
SOFTWARE
PHE B:97 , ASP B:161 , TYR B:174 , TRP B:221 , NAP B:1269 , DTU B:1271 , HOH B:2069
BINDING SITE FOR RESIDUE W16 B1270
07
AC7
SOFTWARE
PHE B:97 , CYS B:168 , PHE B:171 , MET B:213 , TRP B:221 , W16 B:1270
BINDING SITE FOR RESIDUE DTU B1271
08
AC8
SOFTWARE
ARG C:14 , ILE C:15 , TYR C:34 , HIS C:35 , ASN C:36 , SER C:37 , ALA C:61 , ASP C:62 , LEU C:63 , THR C:64 , ASN C:93 , ALA C:94 , SER C:95 , THR C:126 , LEU C:159 , CYS C:160 , ASP C:161 , TYR C:174 , LYS C:178 , PRO C:204 , GLY C:205 , VAL C:206 , SER C:207 , LEU C:208 , W16 C:1270 , HOH C:2002 , HOH C:2003 , HOH C:2004 , HOH C:2006 , HOH C:2018 , HOH C:2046 , HOH C:2048 , HOH C:2049 , HOH C:2100 , HOH C:2101
BINDING SITE FOR RESIDUE NAP C1269
09
AC9
SOFTWARE
PHE C:97 , ASP C:161 , TYR C:174 , TRP C:221 , NAP C:1269 , DTT C:1271 , HOH C:2048
BINDING SITE FOR RESIDUE W16 C1270
10
BC1
SOFTWARE
CYS C:168 , MET C:213 , TRP C:221 , W16 C:1270
BINDING SITE FOR RESIDUE DTT C1271
11
BC2
SOFTWARE
LYS D:13 , ARG D:14 , ILE D:15 , TYR D:34 , HIS D:35 , ASN D:36 , SER D:37 , ALA D:61 , ASP D:62 , LEU D:63 , THR D:64 , ASN D:93 , ALA D:94 , SER D:95 , THR D:126 , LEU D:159 , CYS D:160 , ASP D:161 , TYR D:174 , LYS D:178 , PRO D:204 , GLY D:205 , VAL D:206 , SER D:207 , LEU D:208 , W16 D:1270 , HOH D:2004 , HOH D:2005 , HOH D:2006 , HOH D:2008 , HOH D:2012 , HOH D:2028 , HOH D:2031 , HOH D:2072 , HOH D:2073 , HOH D:2124 , HOH D:2125
BINDING SITE FOR RESIDUE NAP D1269
12
BC3
SOFTWARE
PHE D:97 , ASP D:161 , TYR D:174 , MET D:213 , TRP D:221 , NAP D:1269 , DTT D:1271 , HOH D:2012 , HOH D:2073
BINDING SITE FOR RESIDUE W16 D1270
13
BC4
SOFTWARE
CYS D:168 , MET D:213 , GLU D:217 , TRP D:221 , W16 D:1270 , ACT D:1272
BINDING SITE FOR RESIDUE DTT D1271
14
BC5
SOFTWARE
PHE D:97 , PRO D:99 , DTT D:1271
BINDING SITE FOR RESIDUE ACT D1272
[
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
(0, 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.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2yhia_ (A:)
1b: SCOP_d2yhib_ (B:)
1c: SCOP_d2yhic_ (C:)
1d: SCOP_d2yhid_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Trypanosome (Trypanosoma brucei) [TaxId: 5691]
(13)
1a
d2yhia_
A:
1b
d2yhib_
B:
1c
d2yhic_
C:
1d
d2yhid_
D:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (175 KB)
Header - Asym.Unit
Biol.Unit 1 (166 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
2YHI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help