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.
4M0L
Asym. Unit
Info
Asym.Unit (414 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (72 KB)
Biol.Unit 3 (75 KB)
Biol.Unit 4 (74 KB)
Biol.Unit 5 (74 KB)
Biol.Unit 6 (75 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
GAMMA SUBUNIT OF THE TRANSLATION INITIATION FACTOR 2 FROM SULFOLOBUS SOLFATARICUS COMPLEXED WITH GDP
Authors
:
O. S. Nikonov, E. A. Stolboushkina, V. I. Arkhipova, A. G. Gabdulkhakov A. D. Nikulin, A. M. Lazopulo, S. M. Lazopulo, M. B. Garber, S. V. Nikono
Date
:
01 Aug 13 (Deposition) - 28 Aug 13 (Release) - 12 Mar 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Keywords
:
Aif2, Aif2 Gamma Subunit, G-Protein, Translation, Translation Initiation, Protein Biosynthesis, Rna-Binding, Gtp-Binding, Nucleotide-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
O. Nikonov, E. Stolboushkina, V. Arkhipova, O. Kravchenko, S. Nikonov, M. Garber
Conformational Transitions In The Gamma Subunit Of The Archaeal Translation Initiation Factor 2
Acta Crystallogr. , Sect. D V. 70 658 2014
[
close entry info
]
Hetero Components
(3, 14)
Info
All Hetero Components
1a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
1b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
1c: GUANOSINE-5'-DIPHOSPHATE (GDPc)
1d: GUANOSINE-5'-DIPHOSPHATE (GDPd)
1e: GUANOSINE-5'-DIPHOSPHATE (GDPe)
1f: GUANOSINE-5'-DIPHOSPHATE (GDPf)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
3a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GDP
6
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
2
MG
7
Ligand/Ion
MAGNESIUM ION
3
PO4
1
Ligand/Ion
PHOSPHATE ION
[
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
VAL A:18 , ASP A:19 , GLY A:21 , LYS A:22 , THR A:23 , THR A:24 , ASN A:149 , LYS A:150 , ASP A:152 , VAL A:153 , SER A:184 , ALA A:185 , LEU A:186 , MG A:502 , HOH A:632 , HOH A:646 , HOH A:657
BINDING SITE FOR RESIDUE GDP A 501
02
AC2
SOFTWARE
THR A:23 , GDP A:501 , HOH A:632 , HOH A:644 , HOH A:645 , HOH A:646
BINDING SITE FOR RESIDUE MG A 502
03
AC3
SOFTWARE
VAL B:18 , ASP B:19 , HIS B:20 , GLY B:21 , LYS B:22 , THR B:23 , THR B:24 , ASN B:149 , LYS B:150 , ASP B:152 , VAL B:153 , SER B:184 , ALA B:185 , LEU B:186 , MG B:502 , HOH B:622 , HOH B:645 , HOH B:650
BINDING SITE FOR RESIDUE GDP B 501
04
AC4
SOFTWARE
THR B:23 , GDP B:501 , HOH B:622 , HOH B:625 , HOH B:645
BINDING SITE FOR RESIDUE MG B 502
05
AC5
SOFTWARE
ASP C:19 , HIS C:20 , GLY C:21 , LYS C:22 , THR C:23 , THR C:24 , ASN C:149 , LYS C:150 , ASP C:152 , SER C:184 , ALA C:185 , LEU C:186 , MG C:502 , HOH C:634 , HOH C:643 , HOH C:655
BINDING SITE FOR RESIDUE GDP C 501
06
AC6
SOFTWARE
THR C:23 , GDP C:501 , HOH C:634 , HOH C:643 , HOH C:655 , HOH C:665
BINDING SITE FOR RESIDUE MG C 502
07
AC7
SOFTWARE
THR C:54 , THR C:70 , GLU C:71 , HOH C:607 , HOH C:630
BINDING SITE FOR RESIDUE MG C 503
08
AC8
SOFTWARE
ARG A:404 , ASP D:19 , GLY D:21 , LYS D:22 , THR D:23 , THR D:24 , ASN D:149 , LYS D:150 , ASP D:152 , VAL D:153 , SER D:184 , ALA D:185 , LEU D:186 , MG D:502 , HOH D:617 , HOH D:631 , HOH D:650
BINDING SITE FOR RESIDUE GDP D 501
09
AC9
SOFTWARE
THR D:23 , GDP D:501 , HOH D:617 , HOH D:631 , HOH D:632
BINDING SITE FOR RESIDUE MG D 502
10
BC1
SOFTWARE
HIS E:17 , ASP E:19 , HIS E:20 , GLY E:21 , LYS E:22 , THR E:23 , THR E:24 , ASN E:149 , LYS E:150 , ASP E:152 , VAL E:153 , SER E:184 , ALA E:185 , LEU E:186 , MG E:502 , HOH E:608 , HOH E:621 , HOH E:637 , HOH E:638
BINDING SITE FOR RESIDUE GDP E 501
11
BC2
SOFTWARE
THR E:23 , GDP E:501 , HOH E:621 , HOH E:636 , HOH E:637 , HOH E:638
BINDING SITE FOR RESIDUE MG E 502
12
BC3
SOFTWARE
LEU B:326 , TRP B:327 , ASN B:328 , TYR E:206 , ARG E:207 , ASP E:208
BINDING SITE FOR RESIDUE PO4 E 503
13
BC4
SOFTWARE
ASP F:19 , HIS F:20 , GLY F:21 , LYS F:22 , THR F:23 , THR F:24 , ASN F:149 , LYS F:150 , ASP F:152 , VAL F:153 , SER F:184 , ALA F:185 , LEU F:186 , MG F:502 , HOH F:619
BINDING SITE FOR RESIDUE GDP F 501
14
BC5
SOFTWARE
THR F:23 , GDP F:501 , HOH F:606 , HOH F:615 , HOH F:619
BINDING SITE FOR RESIDUE MG F 502
[
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
(3, 18)
Info
All SCOP Domains
1a: SCOP_d4m0la3 (A:321-415)
1b: SCOP_d4m0lb3 (B:321-415)
1c: SCOP_d4m0lc3 (C:321-415)
1d: SCOP_d4m0ld3 (D:321-415)
1e: SCOP_d4m0le3 (E:321-415)
1f: SCOP_d4m0lf3 (F:321-415)
2a: SCOP_d4m0la2 (A:207-320)
2b: SCOP_d4m0lb2 (B:207-320)
2c: SCOP_d4m0lc2 (C:207-320)
2d: SCOP_d4m0ld2 (D:207-320)
2e: SCOP_d4m0le2 (E:207-320)
2f: SCOP_d4m0lf2 (F:207-320)
3a: SCOP_d4m0la1 (A:2-206)
3b: SCOP_d4m0lb1 (B:2-206)
3c: SCOP_d4m0lc1 (C:2-206)
3d: SCOP_d4m0ld1 (D:2-206)
3e: SCOP_d4m0le1 (E:2-206)
3f: SCOP_d4m0lf1 (F:2-206)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Elongation factor/aminomethyltransferase common domain
(82)
Superfamily
:
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
(67)
Family
:
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
(48)
Protein domain
:
Initiation factor eIF2 gamma subunit
(16)
Sulfolobus solfataricus [TaxId: 2287]
(10)
1a
d4m0la3
A:321-415
1b
d4m0lb3
B:321-415
1c
d4m0lc3
C:321-415
1d
d4m0ld3
D:321-415
1e
d4m0le3
E:321-415
1f
d4m0lf3
F:321-415
Fold
:
Reductase/isomerase/elongation factor common domain
(381)
Superfamily
:
Translation proteins
(218)
Family
:
Elongation factors
(77)
Protein domain
:
Initiation factor eIF2 gamma subunit, domain II
(16)
Sulfolobus solfataricus [TaxId: 2287]
(10)
2a
d4m0la2
A:207-320
2b
d4m0lb2
B:207-320
2c
d4m0lc2
C:207-320
2d
d4m0ld2
D:207-320
2e
d4m0le2
E:207-320
2f
d4m0lf2
F:207-320
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
G proteins
(693)
Protein domain
:
Initiation factor eIF2 gamma subunit, N-terminal (G) domain
(16)
Sulfolobus solfataricus [TaxId: 2287]
(10)
3a
d4m0la1
A:2-206
3b
d4m0lb1
B:2-206
3c
d4m0lc1
C:2-206
3d
d4m0ld1
D:2-206
3e
d4m0le1
E:2-206
3f
d4m0lf1
F:2-206
[
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
Chain E
Chain F
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 (414 KB)
Header - Asym.Unit
Biol.Unit 1 (75 KB)
Header - Biol.Unit 1
Biol.Unit 2 (72 KB)
Header - Biol.Unit 2
Biol.Unit 3 (75 KB)
Header - Biol.Unit 3
Biol.Unit 4 (74 KB)
Header - Biol.Unit 4
Biol.Unit 5 (74 KB)
Header - Biol.Unit 5
Biol.Unit 6 (75 KB)
Header - Biol.Unit 6
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
4M0L
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
