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.
PLEASE WAIT...
Getting 'Exon' information from database.
1M5G
Theor. Model
Info
Theoretical Model (864 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ALL-ATOM HOMOLOGY STRUCTURE OF THE ESCHERICHIA COLI 30S RIBOSOMAL SUBUNIT
Authors
:
C. Tung, S. Joseph, K. Sanbonmatsu
Date
:
09 Jul 02 (Deposition) - 25 Sep 02 (Release) - 25 Sep 02 (Revision)
Method
:
THEORETICAL MODEL
Resolution
:
NOT APPLICABLE
Chains
:
Theor. Model : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
Keywords
:
Homology Model
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Tung, S. Joseph, K. Sanbonmatsu
All-Atom Homology Model Of The Escherichia Coli 30S Ribosomal Subunit
Nat. Struct. Biol. V. 9 750 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(18, 18)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_RS5_ECOLI_001 (R20L, chain E, )
02: VAR_RS5_ECOLI_002 (V21E, chain E, )
03: VAR_RS5_ECOLI_003 (S22P, chain E, )
04: VAR_RS17_ECOLI_001 (H31P, chain Q, )
05: VAR_RS12_ECOLI_001 (K43R, chain L, )
06: VAR_RS12_SALTY_001 (K43R, chain L, )
07: VAR_RS4_ECOLI_001 (Y51D, chain D, )
08: VAR_RS17_ECOLI_002 (S68F, chain Q, )
09: VAR_RS5_SALTY_001 (G102D, chain E, )
10: VAR_RS5_ECOLI_004 (G104R, chain E, )
11: VAR_RS13_ECOLI_001 (N105H, chain M, )
12: VAR_RS13_ECOLI_002 (N105K, chain M, )
13: VAR_RS5_SALTY_002 (G109S, chain E, )
14: VAR_RS5_SALTY_003 (R112C, chain E, )
15: VAR_RS5_ECOLI_005 (R112G, chain E, )
16: VAR_RS5_ECOLI_006 (R112L, chain E, )
17: VAR_RS5_ECOLI_007 (R112S, chain E, )
18: VAR_RS5_ECOLI_008 (E151S, chain E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_RS5_ECOLI_001
*
R
20
L
RS5_ECOLI
---
---
E
R
20
L
02
UniProt
VAR_RS5_ECOLI_002
*
V
21
E
RS5_ECOLI
---
---
E
V
21
E
03
UniProt
VAR_RS5_ECOLI_003
*
S
22
P
RS5_ECOLI
---
---
E
S
22
P
04
UniProt
VAR_RS17_ECOLI_001
*
H
31
P
RS17_ECOLI
---
---
Q
H
31
P
05
UniProt
VAR_RS12_ECOLI_001
*
K
43
R
RS12_ECOLI
---
---
L
K
43
R
06
UniProt
VAR_RS12_SALTY_001
*
K
43
R
RS12_SALTY
---
---
L
K
43
R
07
UniProt
VAR_RS4_ECOLI_001
*
Y
51
D
RS4_ECOLI
---
---
D
Y
51
D
08
UniProt
VAR_RS17_ECOLI_002
*
S
68
F
RS17_ECOLI
---
---
Q
S
68
F
09
UniProt
VAR_RS5_SALTY_001
*
G
102
D
RS5_SALTY
---
---
E
G
102
D
10
UniProt
VAR_RS5_ECOLI_004
*
G
104
R
RS5_ECOLI
---
---
E
G
104
R
11
UniProt
VAR_RS13_ECOLI_001
*
N
105
H
RS13_ECOLI
---
---
M
N
105
H
12
UniProt
VAR_RS13_ECOLI_002
*
N
105
K
RS13_ECOLI
---
---
M
N
105
K
13
UniProt
VAR_RS5_SALTY_002
*
G
109
S
RS5_SALTY
---
---
E
G
109
S
14
UniProt
VAR_RS5_SALTY_003
*
R
112
C
RS5_SALTY
---
---
E
R
112
C
15
UniProt
VAR_RS5_ECOLI_005
*
R
112
G
RS5_ECOLI
---
---
E
R
112
G
16
UniProt
VAR_RS5_ECOLI_006
*
R
112
L
RS5_ECOLI
---
---
E
R
112
L
17
UniProt
VAR_RS5_ECOLI_007
*
R
112
S
RS5_ECOLI
---
---
E
R
112
S
18
UniProt
VAR_RS5_ECOLI_008
*
E
151
S
RS5_ECOLI
---
---
E
E
151
S
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(23, 23)
Info
All PROSITE Patterns/Profiles
01: RIBOSOMAL_S16 (P:2-11,P:2-11,P:2-11,P:2-11)
02: RIBOSOMAL_S13_2 (M:4-111,M:4-111,M:4-111,M:4-111)
03: RIBOSOMAL_S2_1 (B:6-17,B:6-17,B:6-17)
04: S5_DSRBD (E:11-74,E:11-74,E:11-74,E:11-74,E:...)
05: RIBOSOMAL_S7 (G:20-46)
06: RIBOSOMAL_S18 (R:21-44,R:21-44,R:21-44,R:21-44,R:...)
07: RIBOSOMAL_S5 (E:28-60,E:28-60,E:28-60,E:28-60,E:...)
08: RIBOSOMAL_S10 (J:29-44,J:29-44,J:29-44,J:29-44)
09: RIBOSOMAL_S15 (O:39-69)
10: KH_TYPE_2 (C:39-107,C:39-107,C:39-107,C:39-10...)
11: RIBOSOMAL_S12 (L:43-50,L:43-50,L:43-50,L:43-50,L:...)
12: RIBOSOMAL_S6 (F:43-52)
13: RIBOSOMAL_S19 (S:53-77,S:53-77,S:53-77,S:53-77)
14: RIBOSOMAL_S17 (Q:56-68,Q:56-68,Q:56-68,Q:56-68)
15: RIBOSOMAL_S14 (N:63-85,N:63-85,N:63-85,N:63-85)
16: RIBOSOMAL_S9 (I:69-87,I:69-87,I:69-87)
17: RIBOSOMAL_S13_1 (M:87-100,M:87-100,M:87-100,M:87-10...)
18: RIBOSOMAL_S4 (D:94-118,D:94-118,D:94-118)
19: S4 (D:96-156,D:96-156,D:96-156)
20: RIBOSOMAL_S11 (K:97-119,K:97-119,K:97-119,K:97-11...)
21: RIBOSOMAL_S8 (H:100-117,H:100-117,H:100-117,H:10...)
22: RIBOSOMAL_S2_2 (B:158-182,B:158-182,B:158-182)
23: RIBOSOMAL_S3 (C:163-197,C:163-197,C:163-197,C:16...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBOSOMAL_S16
PS00732
Ribosomal protein S16 signature.
RS16_SHIFL
2-11
1
P:2-11
RS16_ECO57
2-11
1
P:2-11
RS16_ECOL6
2-11
1
P:2-11
RS16_ECOLI
2-11
1
P:2-11
2
RIBOSOMAL_S13_2
PS50159
Ribosomal protein S13 family profile.
RS13_ECO57
4-111
1
M:4-111
RS13_ECOL6
4-111
1
M:4-111
RS13_ECOLI
4-111
1
M:4-111
RS13_SHIFL
4-111
1
M:4-111
3
RIBOSOMAL_S2_1
PS00962
Ribosomal protein S2 signature 1.
RS2_ECOL6
6-17
1
B:6-17
RS2_ECOLI
6-17
1
B:6-17
RS2_ECO57
6-17
1
B:6-17
4
S5_DSRBD
PS50881
S5 double stranded RNA-binding domain profile.
RS5_SALTY
11-74
1
E:11-74
RS5_SHIFL
11-74
1
E:11-74
RS5_ECO57
11-74
1
E:11-74
RS5_ECOL6
11-74
1
E:11-74
RS5_ECOLI
11-74
1
E:11-74
RS5_SALTI
11-74
1
E:11-74
5
RIBOSOMAL_S7
PS00052
Ribosomal protein S7 signature.
RS7_ECOLI
20-46
1
G:20-46
6
RIBOSOMAL_S18
PS00057
Ribosomal protein S18 signature.
RS18_ECOL6
21-44
1
R:21-44
RS18_ECOLI
21-44
1
R:21-44
RS18_SALTI
21-44
1
R:21-44
RS18_SHIFL
21-44
1
R:21-44
RS18_ECO57
21-44
1
R:21-44
RS18_PHOLL
21-44
1
R:21-44
7
RIBOSOMAL_S5
PS00585
Ribosomal protein S5 signature.
RS5_SALTY
28-60
1
E:28-60
RS5_SHIFL
28-60
1
E:28-60
RS5_ECO57
28-60
1
E:28-60
RS5_ECOL6
28-60
1
E:28-60
RS5_ECOLI
28-60
1
E:28-60
RS5_SALTI
28-60
1
E:28-60
8
RIBOSOMAL_S10
PS00361
Ribosomal protein S10 signature.
RS10_ECO57
29-44
1
J:29-44
RS10_ECOL6
29-44
1
J:29-44
RS10_ECOLI
29-44
1
J:29-44
RS10_SHIFL
29-44
1
J:29-44
9
RIBOSOMAL_S15
PS00362
Ribosomal protein S15 signature.
RS15_ECO5E
39-69
1
O:39-69
10
KH_TYPE_2
PS50823
Type-2 KH domain profile.
RS3_SALTI
39-107
1
C:39-107
RS3_SALTY
39-107
1
C:39-107
RS3_ECO57
39-107
1
C:39-107
RS3_ECOL6
39-107
1
C:39-107
RS3_ECOLI
39-107
1
C:39-107
11
RIBOSOMAL_S12
PS00055
Ribosomal protein S12 signature.
RS12_ECO57
43-50
1
L:43-50
RS12_ECOL6
43-50
1
L:43-50
RS12_ECOLI
43-50
1
L:43-50
RS12_SHIFL
43-50
1
L:43-50
RS12_SALTI
43-50
1
L:43-50
RS12_SALTY
43-50
1
L:43-50
12
RIBOSOMAL_S6
PS01048
Ribosomal protein S6 signature.
RS6_ECOLI
43-52
1
F:43-52
13
RIBOSOMAL_S19
PS00323
Ribosomal protein S19 signature.
RS19_ECOL6
53-77
1
S:53-77
RS19_ECOLI
53-77
1
S:53-77
RS19_ECO57
53-77
1
S:53-77
RS19_SHIFL
53-77
1
S:53-77
14
RIBOSOMAL_S17
PS00056
Ribosomal protein S17 signature.
RS17_SHIFL
56-68
1
Q:56-68
RS17_ECO57
56-68
1
Q:56-68
RS17_ECOL6
56-68
1
Q:56-68
RS17_ECOLI
56-68
1
Q:56-68
15
RIBOSOMAL_S14
PS00527
Ribosomal protein S14 signature.
RS14_ECO57
63-85
1
N:63-85
RS14_SHIFL
63-85
1
N:63-85
RS14_ECOL6
63-85
1
N:63-85
RS14_ECOLI
63-85
1
N:63-85
16
RIBOSOMAL_S9
PS00360
Ribosomal protein S9 signature.
RS9_ECOL6
69-87
1
I:69-87
RS9_ECOLI
69-87
1
I:69-87
RS9_ECO57
69-87
1
I:69-87
17
RIBOSOMAL_S13_1
PS00646
Ribosomal protein S13 signature.
RS13_ECO57
87-100
1
M:87-100
RS13_ECOL6
87-100
1
M:87-100
RS13_ECOLI
87-100
1
M:87-100
RS13_SHIFL
87-100
1
M:87-100
18
RIBOSOMAL_S4
PS00632
Ribosomal protein S4 signature.
RS4_ECO57
94-118
1
D:94-118
RS4_ECOL6
94-118
1
D:94-118
RS4_ECOLI
94-118
1
D:94-118
19
S4
PS50889
S4 RNA-binding domain profile.
RS4_ECO57
96-156
1
D:96-156
RS4_ECOL6
96-156
1
D:96-156
RS4_ECOLI
96-156
1
D:96-156
20
RIBOSOMAL_S11
PS00054
Ribosomal protein S11 signature.
RS11_ECO57
97-119
1
K:97-119
RS11_SHIFL
97-119
1
K:97-119
RS11_ECOL6
97-119
1
K:97-119
RS11_ECOLI
97-119
1
K:97-119
21
RIBOSOMAL_S8
PS00053
Ribosomal protein S8 signature.
RS8_ECO57
100-117
1
H:100-117
RS8_SHIFL
100-117
1
H:100-117
RS8_SALTI
100-117
1
H:100-117
RS8_SALTY
100-117
1
H:100-117
RS8_ECOL6
100-117
1
H:100-117
RS8_ECOLI
100-117
1
H:100-117
22
RIBOSOMAL_S2_2
PS00963
Ribosomal protein S2 signature 2.
RS2_ECOL6
158-182
1
B:158-182
RS2_ECOLI
158-182
1
B:158-182
RS2_ECO57
158-182
1
B:158-182
23
RIBOSOMAL_S3
PS00548
Ribosomal protein S3 signature.
RS3_SALTI
163-197
1
C:163-197
RS3_SALTY
163-197
1
C:163-197
RS3_ECO57
163-197
1
C:163-197
RS3_ECOL6
163-197
1
C:163-197
RS3_ECOLI
163-197
1
C:163-197
[
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
(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
(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
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
Chain Q
Chain R
Chain S
Chain T
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:
Theoretical Model (864 KB)
Header - Theoretical Model
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
1M5G
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help