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...
Getting 'PROSITE' information from database.
1JNY
Biol. Unit 2
Info
Asym.Unit (147 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (72 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS ELONGATION FACTOR 1 ALPHA IN COMPLEX WITH GDP
Authors
:
L. Vitagliano, M. Masullo, F. Sica, A. Zagari, V. Bocchini
Date
:
26 Jul 01 (Deposition) - 23 Jan 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Gtpase, Alpha/Beta Structure, Protein Biosynthesis, Translation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Vitagliano, M. Masullo, F. Sica, A. Zagari, V. Bocchini
The Crystal Structure Of Sulfolobus Solfataricus Elongation Factor 1Alpha In Complex With Gdp Reveals Novel Features In Nucleotide Binding And Exchange.
Embo J. V. 20 5305 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
1b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GDP
1
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
ASP B:16 , HIS B:17 , GLY B:18 , LYS B:19 , SER B:20 , THR B:21 , ASN B:152 , LYS B:153 , ASP B:155 , LEU B:156 , VAL B:193 , ALA B:194 , PRO B:195 , HOH B:669
BINDING SITE FOR RESIDUE GDP B 600
[
close Site info
]
SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_EF1A_SULSO_001 (S196S, chain B, )
2: VAR_EF1A_SULSO_002 (K203K, chain B, )
3: VAR_EF1A_SULSO_003 (L347L, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_EF1A_SULSO_001
*
A
196
S
EF1A_SULSO
---
---
B
S
196
S
2
UniProt
VAR_EF1A_SULSO_002
*
R
203
K
EF1A_SULSO
---
---
B
K
203
K
3
UniProt
VAR_EF1A_SULSO_003
*
I
347
L
EF1A_SULSO
---
---
B
L
347
L
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: G_TR_1 (B:60-61)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
G_TR_1
PS00301
Translational (tr)-type guanine nucleotide-binding (G) domain signature.
EF1A_SULSO
60-75
1
-
B:60-61
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1jnya2 (A:323-429)
1b: SCOP_d1jnyb2 (B:323-430)
2a: SCOP_d1jnya1 (A:228-322)
2b: SCOP_d1jnyb1 (B:228-322)
3a: SCOP_d1jnya3 (A:4-227)
3b: SCOP_d1jnyb3 (B:4-227)
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
:
Elongation factor eEF-1alpha, C-terminal domain
(8)
Sulfolobus solfataricus [TaxId: 2287]
(2)
1a
d1jnya2
A:323-429
1b
d1jnyb2
B:323-430
Fold
:
Reductase/isomerase/elongation factor common domain
(381)
Superfamily
:
Translation proteins
(218)
Family
:
Elongation factors
(77)
Protein domain
:
Elongation factor eEF-1alpha, domain 2
(8)
Sulfolobus solfataricus [TaxId: 2287]
(2)
2a
d1jnya1
A:228-322
2b
d1jnyb1
B:228-322
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
:
Elongation factor eEF-1alpha, N-terminal (G) domain
(8)
Sulfolobus solfataricus [TaxId: 2287]
(2)
3a
d1jnya3
A:4-227
3b
d1jnyb3
B:4-227
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1jnyA01 (A:4-225)
1b: CATH_1jnyB01 (B:4-225)
2a: CATH_1jnyA03 (A:321-428)
2b: CATH_1jnyB03 (B:321-428)
2c: CATH_1jnyA02 (A:228-316)
2d: CATH_1jnyB02 (B:228-316)
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
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Sulfolobus solfataricus. Organism_taxid: 2287
(1)
1a
1jnyA01
A:4-225
1b
1jnyB01
B:4-225
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Elongation Factor Tu (Ef-tu); domain 3
(323)
Homologous Superfamily
:
Translation factors
(223)
Sulfolobus solfataricus. Organism_taxid: 2287
(1)
2a
1jnyA03
A:321-428
2b
1jnyB03
B:321-428
2c
1jnyA02
A:228-316
2d
1jnyB02
B:228-316
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_GTP_EFTU_1jnyB01 (B:4-266)
1b: PFAM_GTP_EFTU_1jnyB02 (B:4-266)
2a: PFAM_GTP_EFTU_D2_1jnyB03 (B:247-314)
2b: PFAM_GTP_EFTU_D2_1jnyB04 (B:247-314)
3a: PFAM_GTP_EFTU_D3_1jnyB05 (B:319-428)
3b: PFAM_GTP_EFTU_D3_1jnyB06 (B:319-428)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
GTP_EFTU
(39)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(6)
1a
GTP_EFTU-1jnyB01
B:4-266
1b
GTP_EFTU-1jnyB02
B:4-266
Clan
:
no clan defined [family: GTP_EFTU_D2]
(39)
Family
:
GTP_EFTU_D2
(39)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(6)
2a
GTP_EFTU_D2-1jnyB03
B:247-314
2b
GTP_EFTU_D2-1jnyB04
B:247-314
Clan
:
no clan defined [family: GTP_EFTU_D3]
(11)
Family
:
GTP_EFTU_D3
(11)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(2)
3a
GTP_EFTU_D3-1jnyB05
B:319-428
3b
GTP_EFTU_D3-1jnyB06
B:319-428
[
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 B
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 (147 KB)
Header - Asym.Unit
Biol.Unit 1 (75 KB)
Header - Biol.Unit 1
Biol.Unit 2 (72 KB)
Header - Biol.Unit 2
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
1JNY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help