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.
4OQ9
Asym. Unit
Info
Asym.Unit (1.0 MB)
Biol.Unit 1, α-C (4.0 MB)
Biol.Unit 1 (4.0 MB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
SATELLITE TOBACCO MOSAIC VIRUS REFINED TO 1.4 A RESOLUTION USING NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS
Authors
:
S. B. Larson, J. S. Day, A. Mcpherson
Date
:
07 Feb 14 (Deposition) - 10 Sep 14 (Release) - 01 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.45
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,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,1,2,3,4,5,6,7,8
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,1,2,3,4,5,6,7,8 (4x)
Keywords
:
Double-Helix Rna, Protein-Rna Complex, Swiss Jelly-Roll Beta Barrel, Virus-Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. B. Larson, J. S. Day, A. Mcpherson
Satellite Tobacco Mosaic Virus Refined To 1. 4 Angstrom Resolution.
Acta Crystallogr. , Sect. D V. 70 2316 2014
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 41)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
2d: SODIUM ION (NAd)
2e: SODIUM ION (NAe)
2f: SODIUM ION (NAf)
2g: SODIUM ION (NAg)
2h: SODIUM ION (NAh)
2i: SODIUM ION (NAi)
2j: SODIUM ION (NAj)
2k: SODIUM ION (NAk)
2l: SODIUM ION (NAl)
2m: SODIUM ION (NAm)
2n: SODIUM ION (NAn)
2o: SODIUM ION (NAo)
2p: SODIUM ION (NAp)
2q: SODIUM ION (NAq)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
4m: SULFATE ION (SO4m)
4n: SULFATE ION (SO4n)
4o: SULFATE ION (SO4o)
4p: SULFATE ION (SO4p)
4q: SULFATE ION (SO4q)
4r: SULFATE ION (SO4r)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
3
Ligand/Ion
MAGNESIUM ION
2
NA
17
Ligand/Ion
SODIUM ION
3
PO4
3
Ligand/Ion
PHOSPHATE ION
4
SO4
18
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(41, 41)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:115 , ASN A:117 , ASN B:115 , ASN B:117 , ASN C:115 , ASN C:117 , ASN D:115 , ASN D:117 , ASN E:115 , ASN E:117 , SO4 E:201 , MG E:203
BINDING SITE FOR RESIDUE PO4 A 201
02
AC2
SOFTWARE
PHE A:93 , ARG A:95 , HOH A:519 , HOH A:560 , HOH A:636 , HOH A:700 , HOH A:709 , HOH A:743
BINDING SITE FOR RESIDUE SO4 A 202
03
AC3
SOFTWARE
ASP A:68 , ASP O:68 , NA O:202 , HOH O:337 , HOH O:434
BINDING SITE FOR RESIDUE NA A 203
04
AC4
SOFTWARE
ARG B:95 , HOH B:325 , HOH B:367 , HOH B:413
BINDING SITE FOR RESIDUE SO4 B 201
05
AC5
SOFTWARE
ASP B:68 , HOH B:516
BINDING SITE FOR RESIDUE NA B 202
06
AC6
SOFTWARE
ARG B:66 , ASP B:68 , HOH B:326 , HOH B:426
BINDING SITE FOR RESIDUE NA B 203
07
AC7
SOFTWARE
ARG C:95 , HOH C:322 , HOH C:365
BINDING SITE FOR RESIDUE SO4 C 201
08
AC8
SOFTWARE
ASP C:68 , HOH C:498 , ASP N:68 , HOH N:326
BINDING SITE FOR RESIDUE NA C 202
09
AC9
SOFTWARE
PHE D:93 , ARG D:95 , HOH D:325 , HOH D:367 , HOH D:442 , HOH D:496
BINDING SITE FOR RESIDUE SO4 D 201
10
BC1
SOFTWARE
ASP D:68 , ASP H:68 , SER H:69 , NA H:203 , HOH H:325 , HOH H:427
BINDING SITE FOR RESIDUE NA D 202
11
BC2
SOFTWARE
ASN A:117 , PO4 A:201 , HOH A:564 , ASN B:117 , HOH B:371 , ASN C:117 , HOH C:369 , ASN D:117 , HOH D:371 , ASN E:117 , HOH E:306 , HOH E:307 , HOH E:310 , HOH E:315
BINDING SITE FOR RESIDUE SO4 E 201
12
BC3
SOFTWARE
ARG E:95 , HOH E:333 , HOH E:375 , HOH E:500 , HOH E:510 , HOH E:532
BINDING SITE FOR RESIDUE SO4 E 202
13
BC4
SOFTWARE
PO4 A:201
BINDING SITE FOR RESIDUE MG E 203
14
BC5
SOFTWARE
ASP E:68 , ASP F:68 , SER F:69 , NA F:203 , HOH F:325 , HOH F:423
BINDING SITE FOR RESIDUE NA E 204
15
BC6
SOFTWARE
ASP E:68 , HOH E:496 , ASP F:68
BINDING SITE FOR RESIDUE NA E 205
16
BC7
SOFTWARE
PHE F:93 , ARG F:95 , HOH F:324 , HOH F:365 , HOH F:496
BINDING SITE FOR RESIDUE SO4 F 201
17
BC8
SOFTWARE
PO4 H:201
BINDING SITE FOR RESIDUE MG F 202
18
BC9
SOFTWARE
ASP E:68 , SER E:69 , NA E:204 , HOH E:334 , HOH E:432 , ASP F:68
BINDING SITE FOR RESIDUE NA F 203
19
CC1
SOFTWARE
ASN F:117 , HOH F:369 , ASN G:117 , HOH G:307 , HOH G:308 , HOH G:310 , HOH G:378 , HOH G:575 , ASN H:117 , PO4 H:201 , HOH H:371 , ASN I:117 , HOH I:370 , ASN J:117 , HOH J:377
BINDING SITE FOR RESIDUE SO4 G 201
20
CC2
SOFTWARE
PHE G:93 , ARG G:95 , HOH G:330 , HOH G:374
BINDING SITE FOR RESIDUE SO4 G 202
21
CC3
SOFTWARE
ARG G:66 , ASP G:68 , HOH G:331 , HOH G:433
BINDING SITE FOR RESIDUE NA G 203
22
CC4
SOFTWARE
ASN F:115 , ASN F:117 , MG F:202 , ASN G:115 , ASN G:117 , SO4 G:201 , ASN H:115 , ASN H:117 , ASN I:115 , ASN I:117 , ASN J:115 , ASN J:117
BINDING SITE FOR RESIDUE PO4 H 201
23
CC5
SOFTWARE
PHE H:93 , ARG H:95 , HOH H:324 , HOH H:367 , HOH H:566 , HOH H:567
BINDING SITE FOR RESIDUE SO4 H 202
24
CC6
SOFTWARE
ASP D:68 , SER D:69 , NA D:202 , HOH D:326 , HOH D:511 , ASP H:68
BINDING SITE FOR RESIDUE NA H 203
25
CC7
SOFTWARE
PHE I:93 , ARG I:95 , HOH I:324 , HOH I:441 , HOH I:491 , HOH I:493 , HOH I:519 , HOH I:520
BINDING SITE FOR RESIDUE SO4 I 201
26
CC8
SOFTWARE
ASP I:68 , HOH I:422 , ASP M:68 , HOH M:327
BINDING SITE FOR RESIDUE NA I 202
27
CC9
SOFTWARE
ARG J:95 , HOH J:331 , HOH J:373 , HOH J:450 , HOH J:539
BINDING SITE FOR RESIDUE SO4 J 201
28
DC1
SOFTWARE
ARG J:66 , ASP J:68 , HOH J:571 , ASP K:68 , NA K:203 , HOH K:328
BINDING SITE FOR RESIDUE NA J 202
29
DC2
SOFTWARE
ARG K:95 , HOH K:327 , HOH K:445
BINDING SITE FOR RESIDUE SO4 K 201
30
DC3
SOFTWARE
PO4 N:201
BINDING SITE FOR RESIDUE MG K 202
31
DC4
SOFTWARE
ASP J:68 , NA J:202 , HOH J:332 , ASP K:68 , HOH K:307 , HOH K:328
BINDING SITE FOR RESIDUE NA K 203
32
DC5
SOFTWARE
PHE L:93 , ARG L:95 , HOH L:5027 , HOH L:5069 , HOH L:5148 , HOH L:5203 , HOH L:5264
BINDING SITE FOR RESIDUE SO4 L 201
33
DC6
SOFTWARE
ASP L:68 , HOH L:5028
BINDING SITE FOR RESIDUE NA L 202
34
DC7
SOFTWARE
ASN K:117 , HOH K:374 , ASN L:117 , HOH L:5007 , HOH L:5073 , ASN M:117 , HOH M:301 , HOH M:306 , HOH M:373 , ASN N:117 , PO4 N:201 , HOH N:371 , ASN O:117 , HOH O:379
BINDING SITE FOR RESIDUE SO4 M 201
35
DC8
SOFTWARE
PHE M:93 , ARG M:95 , HOH M:326 , HOH M:369 , HOH M:502 , HOH M:531 , HOH M:562 , HOH M:586
BINDING SITE FOR RESIDUE SO4 M 202
36
DC9
SOFTWARE
ASP I:68 , HOH I:325 , ASP M:68 , HOH M:327 , HOH M:427
BINDING SITE FOR RESIDUE NA M 203
37
EC1
SOFTWARE
ASN K:115 , ASN K:117 , MG K:202 , ASN L:115 , ASN L:117 , ASN M:115 , ASN M:117 , SO4 M:201 , ASN N:115 , ASN N:117 , ASN O:115 , ASN O:117
BINDING SITE FOR RESIDUE PO4 N 201
38
EC2
SOFTWARE
PHE N:93 , ARG N:95 , HOH N:325 , HOH N:443 , HOH N:514
BINDING SITE FOR RESIDUE SO4 N 202
39
EC3
SOFTWARE
ASP C:68 , HOH C:323 , ASP N:68 , HOH N:424
BINDING SITE FOR RESIDUE NA N 203
40
EC4
SOFTWARE
PHE O:93 , ARG O:95 , HOH O:317 , HOH O:336 , HOH O:375 , HOH O:456 , HOH O:524 , HOH O:572
BINDING SITE FOR RESIDUE SO4 O 201
41
EC5
SOFTWARE
ASP A:68 , NA A:203 , HOH A:520 , HOH A:725 , ASP O:68
BINDING SITE FOR RESIDUE NA O 202
[
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
(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
Chain U
Chain V
Chain W
Chain X
Chain Y
Chain Z
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
Chain u
Chain v
Chain w
Chain x
Chain y
Chain z
Chain 1
Chain 2
Chain 3
Chain 4
Chain 5
Chain 6
Chain 7
Chain 8
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 (1.0 MB)
Header - Asym.Unit
Biol.Unit 1 (4.0 MB)
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
4OQ9
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
