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.
1WUR
Asym. Unit
Info
Asym.Unit (165 KB)
Biol.Unit 1 (315 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 GTP CYCLOHYDROLASE I COMPLEXED WITH 8-OXO-DGTP
Authors
:
Y. Tanaka, N. Nakagawa, R. Masui, S. Yokoyama, S. Kuramitsu, Riken Str Genomics/Proteomics Initiative (Rsgi)
Date
:
08 Dec 04 (Deposition) - 19 Jul 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.82
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (2x)
Keywords
:
Beta Barrel, Protein-Inhibitor Complex, Hydrolase, Pteridine, Tetrahydrobiopterin, 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. Tanaka, N. Nakagawa, S. Kuramitsu, S. Yokoyama, R. Masui
Novel Reaction Mechanism Of Gtp Cyclohydrolase I. High-Resolution X-Ray Crystallography Of Thermus Thermophilus Hb8 Enzyme Complexed With A Transition State Analogue, The 8-Oxoguanine Derivative
J. Biochem. (Tokyo) V. 138 263 2005
[
close entry info
]
Hetero Components
(2, 10)
Info
All Hetero Components
1a: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOS... (8DGa)
1b: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOS... (8DGb)
1c: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOS... (8DGc)
1d: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOS... (8DGd)
1e: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOS... (8DGe)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
8DG
5
Ligand/Ion
8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2
ZN
5
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:108 , HIS A:111 , CYS A:179 , 8DG A:821
BINDING SITE FOR RESIDUE ZN A 1001
02
AC2
SOFTWARE
CYS B:108 , HIS B:111 , CYS B:179 , 8DG C:822
BINDING SITE FOR RESIDUE ZN B 1002
03
AC3
SOFTWARE
CYS C:108 , HIS C:111 , CYS C:179 , 8DG D:823
BINDING SITE FOR RESIDUE ZN C 1003
04
AC4
SOFTWARE
CYS D:108 , HIS D:111 , CYS D:179 , 8DG D:824
BINDING SITE FOR RESIDUE ZN D 1004
05
AC5
SOFTWARE
8DG A:825 , CYS E:108 , HIS E:111 , CYS E:179
BINDING SITE FOR RESIDUE ZN E 1005
06
AC6
SOFTWARE
CYS A:108 , HIS A:110 , HIS A:111 , VAL A:148 , GLN A:149 , GLU A:150 , HIS A:177 , CYS A:179 , ARG A:183 , ZN A:1001 , HOH A:1012 , HOH A:1038 , HOH A:1060 , HOH A:1079 , ALA B:87 , LEU B:130 , GLY B:131 , LEU B:132 , SER B:133 , LYS B:134 , ARG B:137 , ARG E:64 , HOH E:1029
BINDING SITE FOR RESIDUE 8DG A 821
07
AC7
SOFTWARE
CYS B:108 , HIS B:110 , HIS B:111 , VAL B:148 , GLN B:149 , GLU B:150 , HIS B:177 , CYS B:179 , ARG B:183 , ZN B:1002 , HOH B:1010 , ALA C:87 , LEU C:130 , GLY C:131 , LEU C:132 , SER C:133 , LYS C:134 , ARG C:137 , ARG D:64 , HOH D:1043
BINDING SITE FOR RESIDUE 8DG C 822
08
AC8
SOFTWARE
ARG C:64 , CYS C:108 , HIS C:110 , HIS C:111 , VAL C:148 , GLN C:149 , GLU C:150 , HIS C:177 , CYS C:179 , ARG C:183 , ZN C:1003 , HOH C:1019 , HOH C:1046 , ALA D:87 , LEU D:130 , GLY D:131 , LEU D:132 , SER D:133 , LYS D:134 , ARG D:137 , HOH D:1008 , HOH D:1050
BINDING SITE FOR RESIDUE 8DG D 823
09
AC9
SOFTWARE
ARG B:64 , HOH B:1042 , CYS D:108 , HIS D:110 , HIS D:111 , VAL D:148 , GLN D:149 , GLU D:150 , HIS D:177 , CYS D:179 , ARG D:183 , ZN D:1004 , HOH D:1005 , HOH D:1052 , ALA E:87 , LEU E:130 , GLY E:131 , LEU E:132 , SER E:133 , LYS E:134 , ARG E:137
BINDING SITE FOR RESIDUE 8DG D 824
10
BC1
SOFTWARE
ARG A:64 , ALA A:87 , LEU A:130 , GLY A:131 , LEU A:132 , SER A:133 , LYS A:134 , ARG A:137 , HOH A:1039 , HOH A:1042 , CYS E:108 , HIS E:110 , HIS E:111 , VAL E:148 , GLN E:149 , GLU E:150 , HIS E:177 , CYS E:179 , ARG E:183 , ZN E:1005 , HOH E:1022 , HOH E:1023
BINDING SITE FOR RESIDUE 8DG A 825
[
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, 5)
Info
All SCOP Domains
1a: SCOP_d1wura_ (A:)
1b: SCOP_d1wurb_ (B:)
1c: SCOP_d1wurc_ (C:)
1d: SCOP_d1wurd_ (D:)
1e: SCOP_d1wure_ (E:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
T-fold
(116)
Superfamily
:
Tetrahydrobiopterin biosynthesis enzymes-like
(113)
Family
:
GTP cyclohydrolase I
(15)
Protein domain
:
GTP cyclohydrolase I
(14)
Thermus thermophilus [TaxId: 274]
(3)
1a
d1wura_
A:
1b
d1wurb_
B:
1c
d1wurc_
C:
1d
d1wurd_
D:
1e
d1wure_
E:
[
close SCOP info
]
CATH Domains
(2, 10)
Info
all CATH domains
1a: CATH_1wurA02 (A:86-216)
1b: CATH_1wurB02 (B:86-216)
1c: CATH_1wurC02 (C:86-216)
1d: CATH_1wurD02 (D:86-216)
1e: CATH_1wurE02 (E:86-216)
2a: CATH_1wurA01 (A:32-85)
2b: CATH_1wurB01 (B:32-85)
2c: CATH_1wurC01 (C:32-85)
2d: CATH_1wurD01 (D:32-85)
2e: CATH_1wurE01 (E:33-85)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
GTP Cyclohydrolase I, domain 2
(31)
Homologous Superfamily
:
[code=3.30.1130.10, no name defined]
(31)
Thermus thermophilus. Organism_taxid: 274.
(2)
1a
1wurA02
A:86-216
1b
1wurB02
B:86-216
1c
1wurC02
C:86-216
1d
1wurD02
D:86-216
1e
1wurE02
E:86-216
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
GTP Cyclohydrolase I; Chain A, domain 1
(23)
Homologous Superfamily
:
[code=1.10.286.10, no name defined]
(14)
Thermus thermophilus. Organism_taxid: 274.
(2)
2a
1wurA01
A:32-85
2b
1wurB01
B:32-85
2c
1wurC01
C:32-85
2d
1wurD01
D:32-85
2e
1wurE01
E:33-85
[
close CATH info
]
Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_GTP_cyclohydroI_1wurE01 (E:114-199)
1b: PFAM_GTP_cyclohydroI_1wurE02 (E:114-199)
1c: PFAM_GTP_cyclohydroI_1wurE03 (E:114-199)
1d: PFAM_GTP_cyclohydroI_1wurE04 (E:114-199)
1e: PFAM_GTP_cyclohydroI_1wurE05 (E:114-199)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
THBO-biosyn
(64)
Family
:
GTP_cyclohydroI
(9)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(3)
1a
GTP_cyclohydroI-1wurE01
E:114-199
1b
GTP_cyclohydroI-1wurE02
E:114-199
1c
GTP_cyclohydroI-1wurE03
E:114-199
1d
GTP_cyclohydroI-1wurE04
E:114-199
1e
GTP_cyclohydroI-1wurE05
E:114-199
[
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
Chain E
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 (165 KB)
Header - Asym.Unit
Biol.Unit 1 (315 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
1WUR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
