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.
2QV6
Asym. Unit
Info
Asym.Unit (176 KB)
Biol.Unit 1 (169 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
GTP CYCLOHYDROLASE III FROM M. JANNASCHII (MJ0145) COMPLEXED WITH GTP AND METAL IONS
Authors
:
S. A. Roberts, V. Bandarian
Date
:
07 Aug 07 (Deposition) - 15 Jan 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Enzyme, Gtp, Fapy, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. D. Morrison, S. A. Roberts, A. M. Zegeer, W. R. Montfort, V. Bandarian
A New Use For A Familiar Fold: The X-Ray Crystal Structure Of Gtp-Bound Gtp Cyclohydrolase Iii From Methanocaldococcus Jannaschii Reveals A Two Metal Ion Catalytic Mechanism
Biochemistry V. 47 230 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 16)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: GUANOSINE-5'-TRIPHOSPHATE (GTPa)
2b: GUANOSINE-5'-TRIPHOSPHATE (GTPb)
2c: GUANOSINE-5'-TRIPHOSPHATE (GTPc)
2d: GUANOSINE-5'-TRIPHOSPHATE (GTPd)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
3c: POTASSIUM ION (Kc)
3d: POTASSIUM ION (Kd)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
GTP
4
Ligand/Ion
GUANOSINE-5'-TRIPHOSPHATE
3
K
4
Ligand/Ion
POTASSIUM ION
4
NA
4
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(16, 16)
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)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:230 , GTP A:300 , ARG C:22 , GLU C:24 , HOH C:348
BINDING SITE FOR RESIDUE K A 301
02
AC2
SOFTWARE
ASP A:138 , ILE A:139 , ASP A:183 , GTP A:300 , NA A:303
BINDING SITE FOR RESIDUE CA A 302
03
AC3
SOFTWARE
ASP A:138 , ASP A:183 , ASN A:184 , GTP A:300 , CA A:302 , HOH A:332
BINDING SITE FOR RESIDUE NA A 303
04
AC4
SOFTWARE
ASP B:230 , GTP B:300 , ARG D:22 , GLU D:24 , HOH D:323
BINDING SITE FOR RESIDUE K B 301
05
AC5
SOFTWARE
ASP B:138 , ILE B:139 , ASP B:183 , GTP B:300 , NA B:303
BINDING SITE FOR RESIDUE CA B 302
06
AC6
SOFTWARE
ASP B:138 , ASP B:183 , ASN B:184 , GTP B:300 , CA B:302 , HOH B:344
BINDING SITE FOR RESIDUE NA B 303
07
AC7
SOFTWARE
ARG A:22 , GLU A:24 , ASP C:230 , GTP C:300
BINDING SITE FOR RESIDUE K C 301
08
AC8
SOFTWARE
ASP C:138 , ILE C:139 , ASP C:183 , GTP C:300 , NA C:303
BINDING SITE FOR RESIDUE CA C 302
09
AC9
SOFTWARE
ASP C:138 , ASP C:183 , ASN C:184 , GTP C:300 , CA C:302 , HOH C:355
BINDING SITE FOR RESIDUE NA C 303
10
BC1
SOFTWARE
ARG B:22 , GLU B:24 , HOH B:319 , ASP D:230 , GTP D:300
BINDING SITE FOR RESIDUE K D 301
11
BC2
SOFTWARE
ASP D:138 , ILE D:139 , ASP D:183 , GTP D:300 , NA D:303
BINDING SITE FOR RESIDUE CA D 302
12
BC3
SOFTWARE
ASP D:138 , ASP D:183 , ASN D:184 , GTP D:300 , CA D:302 , HOH D:343
BINDING SITE FOR RESIDUE NA D 303
13
BC4
SOFTWARE
HIS A:136 , ASP A:138 , ILE A:139 , ASN A:141 , ILE A:142 , THR A:143 , ILE A:180 , GLY A:182 , ASP A:183 , ASN A:184 , LYS A:213 , ARG A:237 , K A:301 , CA A:302 , NA A:303 , HOH A:337 , HOH A:338 , TYR C:12 , THR C:16 , GLU C:24 , LEU C:27 , GLN C:28 , ASP C:55 , GLN C:112 , HOH C:310 , HOH C:327
BINDING SITE FOR RESIDUE GTP A 300
14
BC5
SOFTWARE
HIS B:136 , ASP B:138 , ILE B:139 , ASN B:140 , ASN B:141 , ILE B:142 , THR B:143 , ILE B:180 , GLY B:182 , ASP B:183 , ASN B:184 , LYS B:213 , ARG B:237 , K B:301 , CA B:302 , NA B:303 , HOH B:318 , HOH B:344 , HOH B:345 , TYR D:12 , THR D:16 , GLU D:24 , LEU D:27 , GLN D:28 , ASP D:55 , GLN D:112 , HOH D:313
BINDING SITE FOR RESIDUE GTP B 300
15
BC6
SOFTWARE
TYR A:12 , THR A:16 , GLU A:24 , LEU A:27 , GLN A:28 , ASP A:55 , GLN A:112 , LYS B:206 , HIS C:136 , ASP C:138 , ILE C:139 , ASN C:141 , ILE C:142 , THR C:143 , ILE C:180 , GLY C:182 , ASP C:183 , ASN C:184 , LYS C:213 , ARG C:237 , K C:301 , CA C:302 , NA C:303 , HOH C:304 , HOH C:307 , HOH C:311 , HOH C:329 , HOH C:356
BINDING SITE FOR RESIDUE GTP C 300
16
BC7
SOFTWARE
LYS A:206 , TYR B:12 , THR B:16 , GLU B:24 , GLN B:28 , ASP B:55 , GLN B:112 , HOH B:319 , HIS D:136 , ASP D:138 , ILE D:139 , ASN D:141 , ILE D:142 , THR D:143 , ILE D:180 , GLY D:182 , ASP D:183 , ASN D:184 , LYS D:213 , ARG D:237 , K D:301 , CA D:302 , NA D:303 , HOH D:308 , HOH D:310 , HOH D:320
BINDING SITE FOR RESIDUE GTP D 300
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_GGDN_2qv6D01 (D:1-250)
1b: PFAM_GGDN_2qv6D02 (D:1-250)
1c: PFAM_GGDN_2qv6D03 (D:1-250)
1d: PFAM_GGDN_2qv6D04 (D:1-250)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Nucleot_cyclase
(14)
Family
:
GGDN
(1)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth
(1)
1a
GGDN-2qv6D01
D:1-250
1b
GGDN-2qv6D02
D:1-250
1c
GGDN-2qv6D03
D:1-250
1d
GGDN-2qv6D04
D:1-250
[
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 (176 KB)
Header - Asym.Unit
Biol.Unit 1 (169 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
2QV6
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
