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.
3SAG
Asym. Unit
Info
Asym.Unit (138 KB)
Biol.Unit 1 (69 KB)
Biol.Unit 2 (68 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 THE HUMAN RRP6 CATALYTIC DOMAIN WITH D313N MUTATION IN THE ACTIVE SITE
Authors
:
K. Januszyk, Q. Liu, C. D. Lima
Date
:
02 Jun 11 (Deposition) - 06 Jul 11 (Release) - 03 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Exoribonuclease, Rna Exosome, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Januszyk, Q. Liu, C. D. Lima
Activities Of Human Rrp6 And Structure Of The Human Rrp6 Catalytic Domain.
Rna V. 17 1566 2011
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
2a: YTTRIUM (III) ION (YT3a)
2b: YTTRIUM (III) ION (YT3b)
2c: YTTRIUM (III) ION (YT3c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
1
Ligand/Ion
MAGNESIUM ION
2
YT3
3
Ligand/Ion
YTTRIUM (III) ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:73 , HOH A:104 , HOH A:116 , GLU A:296 , GLU A:299 , ASP A:488 , GLU A:489
BINDING SITE FOR RESIDUE YT3 A 1
2
AC2
SOFTWARE
HOH A:28 , ASP A:404 , ASP A:440 , HOH A:630 , HOH A:632
BINDING SITE FOR RESIDUE YT3 A 3
3
AC3
SOFTWARE
HOH B:33 , HOH B:38 , HOH B:40 , ASN B:313 , ASP B:371 , HOH B:611
BINDING SITE FOR RESIDUE MG B 1
4
AC4
SOFTWARE
HOH B:43 , HOH B:128 , GLU B:296 , GLU B:299 , ASP B:488 , GLU B:489
BINDING SITE FOR RESIDUE YT3 B 2
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: HRDC (A:503-583,B:503-583)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HRDC
PS50967
HRDC domain profile.
EXOSX_HUMAN
503-583
2
A:503-583
B:503-583
[
close PROSITE info
]
Exons
(11, 22)
Info
All Exons
Exon 1.6 (A:179-215 | B:179-215)
Exon 1.7 (A:215-253 (gaps) | B:215-253 (gaps...)
Exon 1.8 (A:253-278 | B:253-278)
Exon 1.9 (A:279-315 | B:279-315)
Exon 1.10 (A:316-363 | B:316-363)
Exon 1.11 (A:364-427 | B:364-427)
Exon 1.13a (A:427-479 | B:427-479)
Exon 1.14a (A:480-529 | B:480-529)
Exon 1.14d (A:529-546 | B:529-546)
Exon 1.15b (A:546-583 | B:546-583)
Exon 1.16a (A:584-588 | B:584-588)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.5b/1.6
02: Boundary 1.6/1.7
03: Boundary 1.7/1.8
04: Boundary 1.8/1.9
05: Boundary 1.9/1.10
06: Boundary 1.10/1.11
07: Boundary 1.11/1.13a
08: Boundary 1.13a/1.14a
09: Boundary 1.14a/1.14d
10: Boundary 1.14d/1.15b
11: Boundary 1.15b/1.16a
12: Boundary 1.16a/1.16c
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000376936
1a
ENSE00001472163
chr1:
11159938-11159778
161
EXOSX_HUMAN
1-37
37
0
-
-
1.2
ENST00000376936
2
ENSE00001168316
chr1:
11158213-11158077
137
EXOSX_HUMAN
38-83
46
0
-
-
1.3
ENST00000376936
3
ENSE00001168308
chr1:
11155938-11155815
124
EXOSX_HUMAN
83-124
42
0
-
-
1.5b
ENST00000376936
5b
ENSE00001168299
chr1:
11151654-11151550
105
EXOSX_HUMAN
125-159
35
0
-
-
1.6
ENST00000376936
6
ENSE00001168288
chr1:
11151236-11151071
166
EXOSX_HUMAN
160-215
56
2
A:179-215
B:179-215
37
37
1.7
ENST00000376936
7
ENSE00001168279
chr1:
11150725-11150611
115
EXOSX_HUMAN
215-253
39
2
A:215-253 (gaps)
B:215-253 (gaps)
39
39
1.8
ENST00000376936
8
ENSE00001168272
chr1:
11148255-11148180
76
EXOSX_HUMAN
253-278
26
2
A:253-278
B:253-278
26
26
1.9
ENST00000376936
9
ENSE00001168264
chr1:
11147967-11147857
111
EXOSX_HUMAN
279-315
37
2
A:279-315
B:279-315
37
37
1.10
ENST00000376936
10
ENSE00001168258
chr1:
11147648-11147505
144
EXOSX_HUMAN
316-363
48
2
A:316-363
B:316-363
48
48
1.11
ENST00000376936
11
ENSE00001168251
chr1:
11142935-11142745
191
EXOSX_HUMAN
364-427
64
2
A:364-427
B:364-427
64
64
1.13a
ENST00000376936
13a
ENSE00001168241
chr1:
11141295-11141139
157
EXOSX_HUMAN
427-479
53
2
A:427-479
B:427-479
53
53
1.14a
ENST00000376936
14a
ENSE00001168235
chr1:
11140969-11140821
149
EXOSX_HUMAN
480-529
50
2
A:480-529
B:480-529
50
50
1.14d
ENST00000376936
14d
ENSE00001168225
chr1:
11140606-11140556
51
EXOSX_HUMAN
529-546
18
2
A:529-546
B:529-546
18
18
1.15b
ENST00000376936
15b
ENSE00001168218
chr1:
11139879-11139768
112
EXOSX_HUMAN
546-583
38
2
A:546-583
B:546-583
38
38
1.16a
ENST00000376936
16a
ENSE00001168210
chr1:
11137708-11137658
51
EXOSX_HUMAN
584-600
17
2
A:584-588
B:584-588
5
5
1.16c
ENST00000376936
16c
ENSE00001168203
chr1:
11137500-11137422
79
EXOSX_HUMAN
601-627
27
0
-
-
1.16f
ENST00000376936
16f
ENSE00001168196
chr1:
11137005-11136899
107
EXOSX_HUMAN
627-662
36
0
-
-
1.17b
ENST00000376936
17b
ENSE00001168190
chr1:
11134383-11134288
96
EXOSX_HUMAN
663-694
32
0
-
-
1.18
ENST00000376936
18
ENSE00001168157
chr1:
11134065-11133991
75
EXOSX_HUMAN
695-719
25
0
-
-
1.19c
ENST00000376936
19c
ENSE00001168184
chr1:
11132228-11132144
85
EXOSX_HUMAN
720-748
29
0
-
-
1.19e
ENST00000376936
19e
ENSE00001168178
chr1:
11131030-11130957
74
EXOSX_HUMAN
748-772
25
0
-
-
1.20
ENST00000376936
20
ENSE00001168173
chr1:
11129787-11129616
172
EXOSX_HUMAN
773-830
58
0
-
-
1.21c
ENST00000376936
21c
ENSE00001168168
chr1:
11128763-11128702
62
EXOSX_HUMAN
830-850
21
0
-
-
1.22
ENST00000376936
22
ENSE00001168163
chr1:
11128141-11128065
77
EXOSX_HUMAN
851-876
26
0
-
-
1.23c
ENST00000376936
23c
ENSE00001918071
chr1:
11126805-11126675
131
EXOSX_HUMAN
876-885
10
0
-
-
[
close EXON info
]
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
(2, 4)
Info
all PFAM domains
1a: PFAM_HRDC_3sagB01 (B:506-573)
1b: PFAM_HRDC_3sagB02 (B:506-573)
2a: PFAM_DNA_pol_A_exo1_3sagB03 (B:288-456)
2b: PFAM_DNA_pol_A_exo1_3sagB04 (B:288-456)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HRDC-like
(19)
Family
:
HRDC
(8)
Homo sapiens (Human)
(5)
1a
HRDC-3sagB01
B:506-573
1b
HRDC-3sagB02
B:506-573
Clan
:
RNase_H
(288)
Family
:
DNA_pol_A_exo1
(16)
Homo sapiens (Human)
(3)
2a
DNA_pol_A_exo1-3sagB03
B:288-456
2b
DNA_pol_A_exo1-3sagB04
B:288-456
[
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 (138 KB)
Header - Asym.Unit
Biol.Unit 1 (69 KB)
Header - Biol.Unit 1
Biol.Unit 2 (68 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
3SAG
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help