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.
3GN1
Asym. Unit
Info
Asym.Unit (183 KB)
Biol.Unit 1 (174 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR (NADP+) AND INHIBITOR (DDD00067116)
Authors
:
L. B. Tulloch, R. Brenk, W. N. Hunter
Date
:
16 Mar 09 (Deposition) - 29 Dec 09 (Release) - 07 Sep 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Pteridine Reductase, Ptr1, Trypanosoma Brucei, Short Chain Dehydrogenase, Inhibitor, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. P. Mpamhanga, D. Spinks, L. B. Tulloch, E. J. Shanks, D. A. Robinson, I. T. Collie, A. H. Fairlamb, P. G. Wyatt, J. A. Frearson, W. N. Hunter, I. H. Gilbert, R. Brenk
One Scaffold, Three Binding Modes: Novel And Selective Pteridine Reductase 1 Inhibitors Derived From Fragment Hits Discovered By Virtual Screening.
J. Med. Chem. V. 52 4454 2009
[
close entry info
]
Hetero Components
(4, 13)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
2a: 1H-BENZIMIDAZOL-2-AMINE (AX7a)
2b: 1H-BENZIMIDAZOL-2-AMINE (AX7b)
2c: 1H-BENZIMIDAZOL-2-AMINE (AX7c)
3a: S-OXY CYSTEINE (CSXa)
3b: S-OXY CYSTEINE (CSXb)
3c: S-OXY CYSTEINE (CSXc)
3d: S-OXY CYSTEINE (CSXd)
4a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
4b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
4c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
4d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
AX7
3
Ligand/Ion
1H-BENZIMIDAZOL-2-AMINE
3
CSX
4
Mod. Amino Acid
S-OXY CYSTEINE
4
NAP
4
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
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 , AX7 A:271 , HOH A:293 , HOH A:296 , HOH A:315 , HOH A:320 , HOH A:329 , HOH A:372 , HOH A:384 , HOH A:417 , HOH A:471
BINDING SITE FOR RESIDUE NAP A 269
2
AC2
SOFTWARE
PHE A:97 , ASP A:161 , TYR A:174 , NAP A:269 , HOH A:430
BINDING SITE FOR RESIDUE AX7 A 271
3
AC3
SOFTWARE
LYS A:13 , ARG A:14 , ARG A:17 , HOH A:375 , HOH A:385 , HOH A:400
BINDING SITE FOR RESIDUE ACT A 270
4
AC4
SOFTWARE
ARG B:14 , ILE B:15 , HIS B:33 , 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 , HOH B:490 , HOH B:494 , HOH B:498 , HOH B:517 , HOH B:522 , HOH B:544 , HOH B:556 , HOH B:573 , HOH B:584 , HOH B:622
BINDING SITE FOR RESIDUE NAP B 269
5
AC5
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 , AX7 C:271 , HOH C:479 , HOH C:480 , HOH C:497 , HOH C:570 , HOH C:608 , HOH C:613 , HOH C:615 , HOH C:675
BINDING SITE FOR RESIDUE NAP C 269
6
AC6
SOFTWARE
PHE C:97 , ASP C:161 , TYR C:174 , NAP C:269 , HOH C:615 , HOH C:676
BINDING SITE FOR RESIDUE AX7 C 271
7
AC7
SOFTWARE
TYR B:34 , VAL B:58 , HOH B:695 , VAL C:57 , VAL C:58 , HOH C:463
BINDING SITE FOR RESIDUE ACT C 270
8
AC8
SOFTWARE
ARG D:14 , ILE D:15 , HIS D:33 , 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 , TYR D:174 , LYS D:178 , PRO D:204 , GLY D:205 , VAL D:206 , SER D:207 , LEU D:208 , AX7 D:270 , HOH D:387 , HOH D:395 , HOH D:423 , HOH D:453 , HOH D:514 , HOH D:520 , HOH D:527 , HOH D:536 , HOH D:553 , HOH D:563
BINDING SITE FOR RESIDUE NAP D 269
9
AC9
SOFTWARE
PHE D:97 , ASP D:161 , TYR D:174 , NAP D:269 , HOH D:514 , HOH D:546
BINDING SITE FOR RESIDUE AX7 D 270
[
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_d3gn1a_ (A:)
1b: SCOP_d3gn1b_ (B:)
1c: SCOP_d3gn1c_ (C:)
1d: SCOP_d3gn1d_ (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
:
Tyrosine-dependent oxidoreductases
(503)
Protein domain
:
Dihydropteridin reductase (pteridine reductase)
(24)
Trypanosoma brucei [TaxId: 5702]
(7)
1a
d3gn1a_
A:
1b
d3gn1b_
B:
1c
d3gn1c_
C:
1d
d3gn1d_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3gn1B00 (B:2-268)
1b: CATH_3gn1C00 (C:2-268)
1c: CATH_3gn1A00 (A:2-268)
1d: CATH_3gn1D00 (D:2-268)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Trypanosoma brucei brucei. Organism_taxid: 5702.
(6)
1a
3gn1B00
B:2-268
1b
3gn1C00
C:2-268
1c
3gn1A00
A:2-268
1d
3gn1D00
D:2-268
[
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 (183 KB)
Header - Asym.Unit
Biol.Unit 1 (174 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
3GN1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help