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.
1L9A
Asym. Unit
Info
Asym.Unit (77 KB)
Biol.Unit 1 (71 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 SRP19 IN COMPLEX WITH THE S DOMAIN OF SIGNAL RECOGNITION PARTICLE RNA
Authors
:
C. Oubridge, A. Kuglstatter, L. Jovine, K. Nagai
Date
:
22 Mar 02 (Deposition) - 28 Jun 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Protein-Rna Complex, Ribonucleoprotein, Srp, Signal Recognition Particle, Tetraloop, Signaling Protein/Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Oubridge, A. Kuglstatter, L. Jovine, K. Nagai
Crystal Structure Of Srp19 In Complex With The S Domain Of Srp Rna And Its Implication For The Assembly Of The Signal Recognition Particle.
Mol. Cell V. 9 1251 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 26)
Info
All Hetero Components
1a: CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC... (CCCa)
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)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
2j: MAGNESIUM ION (MGj)
2k: MAGNESIUM ION (MGk)
2l: MAGNESIUM ION (MGl)
2m: MAGNESIUM ION (MGm)
2n: MAGNESIUM ION (MGn)
2o: MAGNESIUM ION (MGo)
2p: MAGNESIUM ION (MGp)
2q: MAGNESIUM ION (MGq)
2r: MAGNESIUM ION (MGr)
2s: MAGNESIUM ION (MGs)
2t: MAGNESIUM ION (MGt)
2u: MAGNESIUM ION (MGu)
2v: MAGNESIUM ION (MGv)
2w: MAGNESIUM ION (MGw)
2x: MAGNESIUM ION (MGx)
3a: METHYL MERCURY ION (MMCa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CCC
1
Mod. Nucleotide
CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2
MG
24
Ligand/Ion
MAGNESIUM ION
3
MMC
1
Ligand/Ion
METHYL MERCURY ION
[
close Hetero Component info
]
Sites
(24, 24)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
A B:205
BINDING SITE FOR RESIDUE MG B 101
02
AC2
SOFTWARE
U B:218
BINDING SITE FOR RESIDUE MG B 102
03
AC3
SOFTWARE
G B:193
BINDING SITE FOR RESIDUE MG B 103
04
AC4
SOFTWARE
G B:187
BINDING SITE FOR RESIDUE MG B 104
05
AC5
SOFTWARE
A B:215
BINDING SITE FOR RESIDUE MG B 105
06
AC6
SOFTWARE
C B:219
BINDING SITE FOR RESIDUE MG B 106
07
AC7
SOFTWARE
GLU A:22 , HOH B:18 , HOH B:19
BINDING SITE FOR RESIDUE MG A 107
08
AC8
SOFTWARE
G B:209 , G B:210
BINDING SITE FOR RESIDUE MG B 108
09
AC9
SOFTWARE
G B:164 , G B:165
BINDING SITE FOR RESIDUE MG B 110
10
BC1
SOFTWARE
HOH B:20 , U B:226 , G B:227
BINDING SITE FOR RESIDUE MG B 111
11
BC2
SOFTWARE
A B:215
BINDING SITE FOR RESIDUE MG B 240
12
BC3
SOFTWARE
HOH B:16 , G B:152
BINDING SITE FOR RESIDUE MG B 241
13
BC4
SOFTWARE
HOH B:11 , HOH B:12 , HOH B:13 , HOH B:14 , C B:170 , A B:172
BINDING SITE FOR RESIDUE MG B 242
14
BC5
SOFTWARE
HOH B:12 , HOH B:14 , U B:171 , A B:172
BINDING SITE FOR RESIDUE MG B 243
15
BC6
SOFTWARE
G B:227 , A B:228
BINDING SITE FOR RESIDUE MG B 244
16
BC7
SOFTWARE
G B:164
BINDING SITE FOR RESIDUE MG B 245
17
BC8
SOFTWARE
U B:166 , U B:167
BINDING SITE FOR RESIDUE MG B 246
18
BC9
SOFTWARE
G B:237 , U B:238
BINDING SITE FOR RESIDUE MG B 247
19
CC1
SOFTWARE
C B:225 , U B:226
BINDING SITE FOR RESIDUE MG B 248
20
CC2
SOFTWARE
A B:208 , G B:209
BINDING SITE FOR RESIDUE MG B 249
21
CC3
SOFTWARE
G B:206 , C B:207
BINDING SITE FOR RESIDUE MG B 250
22
CC4
SOFTWARE
HOH B:5
BINDING SITE FOR RESIDUE MG B 251
23
CC5
SOFTWARE
ASP A:33
BINDING SITE FOR RESIDUE MG A 124
24
CC6
SOFTWARE
TYR A:68 , CYS A:74 , LEU A:75
BINDING SITE FOR RESIDUE MMC A 88
[
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, 1)
Info
All SCOP Domains
1a: SCOP_d1l9aa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
SRP19
(11)
Superfamily
:
SRP19
(11)
Family
:
SRP19
(9)
Protein domain
:
SRP19
(9)
Methanococcus jannaschii [TaxId: 2190]
(3)
1a
d1l9aa_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1l9aA00 (A:1-87)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Phenylalanyl-tRNA Synthetase; Chain B, domain 1
(22)
Homologous Superfamily
:
SRP19
(8)
[unclassified]
(2)
1a
1l9aA00
A:1-87
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_SRP19_1l9aA01 (A:1-87)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: SRP19]
(9)
Family
:
SRP19
(9)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth
(3)
1a
SRP19-1l9aA01
A:1-87
[
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
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 (77 KB)
Header - Asym.Unit
Biol.Unit 1 (71 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
1L9A
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help