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.
2C38
Biol. Unit 3
Info
Asym.Unit (953 KB)
Biol.Unit 1 (243 KB)
Biol.Unit 2 (245 KB)
Biol.Unit 3 (244 KB)
Biol.Unit 4 (243 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
RNASE PH CORE OF THE ARCHAEAL EXOSOME IN COMPLEX WITH A5 RNA
Authors
:
E. Lorentzen, E. Conti
Date
:
04 Oct 05 (Deposition) - 23 Nov 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Biol. Unit 3: M,N,O,P,Q,R (1x)
Biol. Unit 4: S,T,U,V,W,X (1x)
Keywords
:
Exosome, Rnase Ph, Rrp41, Rrp42, Phosphorolytic, Exoribonuclease, Rna Degradation, Archaeal, Hydrolase, Exonuclease, Nuclease
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Lorentzen, E. Conti
Structural Basis Of 3' End Rna Recognition And Exoribonucleolytic Cleavage By An Exosome Rnase Ph Core.
Mol. Cell V. 20 473 2005
[
close entry info
]
Hetero Components
(1, 4)
Info
All Hetero Components
1a: ADENOSINE MONOPHOSPHATE (AMPa)
1aa: ADENOSINE MONOPHOSPHATE (AMPaa)
1ab: ADENOSINE MONOPHOSPHATE (AMPab)
1b: ADENOSINE MONOPHOSPHATE (AMPb)
1c: ADENOSINE MONOPHOSPHATE (AMPc)
1d: ADENOSINE MONOPHOSPHATE (AMPd)
1e: ADENOSINE MONOPHOSPHATE (AMPe)
1f: ADENOSINE MONOPHOSPHATE (AMPf)
1g: ADENOSINE MONOPHOSPHATE (AMPg)
1h: ADENOSINE MONOPHOSPHATE (AMPh)
1i: ADENOSINE MONOPHOSPHATE (AMPi)
1j: ADENOSINE MONOPHOSPHATE (AMPj)
1k: ADENOSINE MONOPHOSPHATE (AMPk)
1l: ADENOSINE MONOPHOSPHATE (AMPl)
1m: ADENOSINE MONOPHOSPHATE (AMPm)
1n: ADENOSINE MONOPHOSPHATE (AMPn)
1o: ADENOSINE MONOPHOSPHATE (AMPo)
1p: ADENOSINE MONOPHOSPHATE (AMPp)
1q: ADENOSINE MONOPHOSPHATE (AMPq)
1r: ADENOSINE MONOPHOSPHATE (AMPr)
1s: ADENOSINE MONOPHOSPHATE (AMPs)
1t: ADENOSINE MONOPHOSPHATE (AMPt)
1u: ADENOSINE MONOPHOSPHATE (AMPu)
1v: ADENOSINE MONOPHOSPHATE (AMPv)
1w: ADENOSINE MONOPHOSPHATE (AMPw)
1x: ADENOSINE MONOPHOSPHATE (AMPx)
1y: ADENOSINE MONOPHOSPHATE (AMPy)
1z: ADENOSINE MONOPHOSPHATE (AMPz)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
2h: CHLORIDE ION (CLh)
2i: CHLORIDE ION (CLi)
2j: CHLORIDE ION (CLj)
2k: CHLORIDE ION (CLk)
2l: CHLORIDE ION (CLl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AMP
4
Ligand/Ion
ADENOSINE MONOPHOSPHATE
2
CL
-1
Ligand/Ion
CHLORIDE ION
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC7 (SOFTWARE)
2: AC8 (SOFTWARE)
3: AC9 (SOFTWARE)
4: BC1 (SOFTWARE)
5: DC2 (SOFTWARE)
6: DC3 (SOFTWARE)
7: DC4 (SOFTWARE)
8: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC7
SOFTWARE
ARG N:99 , GLY N:137 , SER N:138 , ARG N:139 , AMP N:404
BINDING SITE FOR RESIDUE CL N 301
2
AC8
SOFTWARE
ARG P:2 , ARG P:99 , GLY P:137 , SER P:138 , ARG P:139
BINDING SITE FOR RESIDUE CL P 301
3
AC9
SOFTWARE
ARG R:99 , GLY R:137 , SER R:138 , ARG R:139
BINDING SITE FOR RESIDUE CL R 301
4
BC1
SOFTWARE
ARG R:2 , ARG T:99 , GLY T:137 , SER T:138 , ARG T:139
BINDING SITE FOR RESIDUE CL T 301
5
DC2
SOFTWARE
TYR M:75 , LEU M:84 , ILE M:85 , ARG N:98 , AMP N:402
BINDING SITE FOR RESIDUE AMP N 401
6
DC3
SOFTWARE
ARG M:112 , ASP M:115 , ARG N:98 , AMP N:401 , AMP N:403
BINDING SITE FOR RESIDUE AMP N 402
7
DC4
SOFTWARE
ARG M:112 , ARG M:116 , ASP N:182 , AMP N:402 , AMP N:404
BINDING SITE FOR RESIDUE AMP N 403
8
DC5
SOFTWARE
MET N:83 , THR N:88 , ARG N:99 , ALA N:136 , SER N:138 , ARG N:139 , GLU N:179 , ASP N:182 , ASP N:188 , CL N:301 , AMP N:403
BINDING SITE FOR RESIDUE AMP N 404
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 48)
Info
All SCOP Domains
1a: SCOP_d2c38a2 (A:192-275)
1b: SCOP_d2c38c2 (C:192-275)
1c: SCOP_d2c38e2 (E:192-275)
1d: SCOP_d2c38g2 (G:192-275)
1e: SCOP_d2c38i2 (I:192-275)
1f: SCOP_d2c38k2 (K:192-275)
1g: SCOP_d2c38m2 (M:192-275)
1h: SCOP_d2c38o2 (O:192-275)
1i: SCOP_d2c38q2 (Q:192-275)
1j: SCOP_d2c38s2 (S:192-275)
1k: SCOP_d2c38u2 (U:192-274)
1l: SCOP_d2c38w2 (W:192-275)
2a: SCOP_d2c38b2 (B:156-248)
2b: SCOP_d2c38d2 (D:156-248)
2c: SCOP_d2c38f2 (F:156-248)
2d: SCOP_d2c38h2 (H:156-248)
2e: SCOP_d2c38j2 (J:156-248)
2f: SCOP_d2c38l2 (L:156-248)
2g: SCOP_d2c38n2 (N:156-248)
2h: SCOP_d2c38p2 (P:156-248)
2i: SCOP_d2c38r2 (R:156-248)
2j: SCOP_d2c38t2 (T:156-248)
2k: SCOP_d2c38v2 (V:156-247)
2l: SCOP_d2c38x2 (X:156-248)
3a: SCOP_d2c38a1 (A:1-191)
3b: SCOP_d2c38c1 (C:1-191)
3c: SCOP_d2c38e1 (E:1-191)
3d: SCOP_d2c38g1 (G:1-191)
3e: SCOP_d2c38i1 (I:1-191)
3f: SCOP_d2c38k1 (K:1-191)
3g: SCOP_d2c38m1 (M:1-191)
3h: SCOP_d2c38o1 (O:1-191)
3i: SCOP_d2c38q1 (Q:1-191)
3j: SCOP_d2c38s1 (S:1-191)
3k: SCOP_d2c38u1 (U:1-191)
3l: SCOP_d2c38w1 (W:1-191)
4a: SCOP_d2c38b1 (B:8-155)
4b: SCOP_d2c38d1 (D:8-155)
4c: SCOP_d2c38f1 (F:8-155)
4d: SCOP_d2c38h1 (H:8-155)
4e: SCOP_d2c38j1 (J:8-155)
4f: SCOP_d2c38l1 (L:8-155)
4g: SCOP_d2c38n1 (N:8-155)
4h: SCOP_d2c38p1 (P:8-155)
4i: SCOP_d2c38r1 (R:8-155)
4j: SCOP_d2c38t1 (T:8-155)
4k: SCOP_d2c38v1 (V:9-155)
4l: SCOP_d2c38x1 (X:8-155)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ribonuclease PH domain 2-like
(52)
Superfamily
:
Ribonuclease PH domain 2-like
(52)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Sulfolobus solfataricus [TaxId: 2287]
(4)
1a
d2c38a2
A:192-275
1b
d2c38c2
C:192-275
1c
d2c38e2
E:192-275
1d
d2c38g2
G:192-275
1e
d2c38i2
I:192-275
1f
d2c38k2
K:192-275
1g
d2c38m2
M:192-275
1h
d2c38o2
O:192-275
1i
d2c38q2
Q:192-275
1j
d2c38s2
S:192-275
1k
d2c38u2
U:192-274
1l
d2c38w2
W:192-275
Family
:
Ribonuclease PH domain 2-like
(41)
Protein domain
:
Exosome complex exonuclease 1, ECX1
(11)
Sulfolobus solfataricus [TaxId: 2287]
(9)
2a
d2c38b2
B:156-248
2b
d2c38d2
D:156-248
2c
d2c38f2
F:156-248
2d
d2c38h2
H:156-248
2e
d2c38j2
J:156-248
2f
d2c38l2
L:156-248
2g
d2c38n2
N:156-248
2h
d2c38p2
P:156-248
2i
d2c38r2
R:156-248
2j
d2c38t2
T:156-248
2k
d2c38v2
V:156-247
2l
d2c38x2
X:156-248
Fold
:
Ribosomal protein S5 domain 2-like
(306)
Superfamily
:
Ribosomal protein S5 domain 2-like
(306)
Family
:
Ribonuclease PH domain 1-like
(45)
Protein domain
:
automated matches
(6)
Sulfolobus solfataricus [TaxId: 2287]
(4)
3a
d2c38a1
A:1-191
3b
d2c38c1
C:1-191
3c
d2c38e1
E:1-191
3d
d2c38g1
G:1-191
3e
d2c38i1
I:1-191
3f
d2c38k1
K:1-191
3g
d2c38m1
M:1-191
3h
d2c38o1
O:1-191
3i
d2c38q1
Q:1-191
3j
d2c38s1
S:1-191
3k
d2c38u1
U:1-191
3l
d2c38w1
W:1-191
Protein domain
:
Exosome complex exonuclease 1, ECX1
(11)
Sulfolobus solfataricus [TaxId: 2287]
(9)
4a
d2c38b1
B:8-155
4b
d2c38d1
D:8-155
4c
d2c38f1
F:8-155
4d
d2c38h1
H:8-155
4e
d2c38j1
J:8-155
4f
d2c38l1
L:8-155
4g
d2c38n1
N:8-155
4h
d2c38p1
P:8-155
4i
d2c38r1
R:8-155
4j
d2c38t1
T:8-155
4k
d2c38v1
V:9-155
4l
d2c38x1
X:8-155
[
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 M
Chain N
Chain O
Chain P
Chain Q
Chain R
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 (953 KB)
Header - Asym.Unit
Biol.Unit 1 (243 KB)
Header - Biol.Unit 1
Biol.Unit 2 (245 KB)
Header - Biol.Unit 2
Biol.Unit 3 (244 KB)
Header - Biol.Unit 3
Biol.Unit 4 (243 KB)
Header - Biol.Unit 4
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
2C38
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help