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.
3J1F
Asym. Unit
Info
Asym.Unit (1.2 MB)
Biol.Unit 1, α-C (1.2 MB)
Biol.Unit 1 (1.2 MB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYO-EM STRUCTURE OF 9-FOLD SYMMETRIC RATCPN-BETA IN ATP-BINDING STATE
Authors
:
K. Zhang, L. Wang, Y. X. Liu, X. Wang, B. Gao, Z. J. Hu, G. Ji, K. Y. Chan, K. S Z. Y. Dong, F. Sun
Date
:
06 Feb 12 (Deposition) - 07 Aug 13 (Release) - 07 Aug 13 (Revision)
Method
:
ELECTRON MICROSCOPY
Resolution
:
6.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S
Biol. Unit 1: A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S (1x)
Keywords
:
Group Ii Chaperonin, Chaperone
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Zhang, L. Wang, Y. Liu, K. Y. Chan, X. Pang, K. Schulten, Z. Dong, F. Su
Flexible Interwoven Termini Determine The Thermal Stability Of Thermosomes.
Protein Cell V. 4 432 2013
[
close entry info
]
Hetero Components
(2, 36)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
1c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
1d: ADENOSINE-5'-TRIPHOSPHATE (ATPd)
1e: ADENOSINE-5'-TRIPHOSPHATE (ATPe)
1f: ADENOSINE-5'-TRIPHOSPHATE (ATPf)
1g: ADENOSINE-5'-TRIPHOSPHATE (ATPg)
1h: ADENOSINE-5'-TRIPHOSPHATE (ATPh)
1i: ADENOSINE-5'-TRIPHOSPHATE (ATPi)
1j: ADENOSINE-5'-TRIPHOSPHATE (ATPj)
1k: ADENOSINE-5'-TRIPHOSPHATE (ATPk)
1l: ADENOSINE-5'-TRIPHOSPHATE (ATPl)
1m: ADENOSINE-5'-TRIPHOSPHATE (ATPm)
1n: ADENOSINE-5'-TRIPHOSPHATE (ATPn)
1o: ADENOSINE-5'-TRIPHOSPHATE (ATPo)
1p: ADENOSINE-5'-TRIPHOSPHATE (ATPp)
1q: ADENOSINE-5'-TRIPHOSPHATE (ATPq)
1r: ADENOSINE-5'-TRIPHOSPHATE (ATPr)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
18
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
MG
18
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(36, 36)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:50 , PRO A:52 , ALA A:101 , ASP A:102 , GLY A:103 , THR A:104 , LYS A:105 , THR A:106 , GLY A:417 , GLY A:418 , LEU A:489 , TYR A:490 , GLU A:504 , LYS A:509 , MG A:801
BINDING SITE FOR RESIDUE ATP A 800
02
AC2
SOFTWARE
ASP A:102 , ATP A:800
BINDING SITE FOR RESIDUE MG A 801
03
AC3
SOFTWARE
TYR B:50 , PRO B:52 , ASP B:102 , GLY B:103 , THR B:104 , LYS B:105 , THR B:106 , GLY B:418 , ILE B:487 , LEU B:489 , MET B:497 , GLU B:504 , LYS B:509 , MG B:801
BINDING SITE FOR RESIDUE ATP B 800
04
AC4
SOFTWARE
ASP B:102 , ATP B:800
BINDING SITE FOR RESIDUE MG B 801
05
AC5
SOFTWARE
TYR C:50 , PRO C:52 , ASP C:102 , GLY C:103 , THR C:104 , LYS C:105 , THR C:106 , GLY C:417 , GLY C:418 , LEU C:489 , VAL C:502 , GLU C:504 , LYS C:509 , MG C:801
BINDING SITE FOR RESIDUE ATP C 800
06
AC6
SOFTWARE
ASP C:102 , GLY C:103 , ATP C:800
BINDING SITE FOR RESIDUE MG C 801
07
AC7
SOFTWARE
TYR D:50 , GLY D:51 , ASP D:102 , GLY D:103 , THR D:104 , LYS D:105 , THR D:106 , LYS D:172 , GLY D:417 , GLY D:418 , ILE D:487 , LEU D:489 , MET D:497 , GLU D:504 , MG D:801
BINDING SITE FOR RESIDUE ATP D 800
08
AC8
SOFTWARE
ASP D:102 , ATP D:800
BINDING SITE FOR RESIDUE MG D 801
09
AC9
SOFTWARE
TYR E:50 , ASP E:102 , GLY E:103 , THR E:104 , LYS E:105 , THR E:106 , GLY E:417 , GLY E:418 , ILE E:487 , LEU E:489 , MET E:497 , GLU E:504 , LYS E:509 , MG E:801
BINDING SITE FOR RESIDUE ATP E 800
10
BC1
SOFTWARE
ASP E:102 , ATP E:800
BINDING SITE FOR RESIDUE MG E 801
11
BC2
SOFTWARE
TYR F:50 , GLY F:51 , PRO F:52 , ALA F:101 , ASP F:102 , GLY F:103 , THR F:104 , LYS F:105 , THR F:106 , GLY F:418 , ILE F:487 , LEU F:489 , GLU F:504 , LYS F:509 , MG F:801
BINDING SITE FOR RESIDUE ATP F 800
12
BC3
SOFTWARE
ASP F:102 , ATP F:800
BINDING SITE FOR RESIDUE MG F 801
13
BC4
SOFTWARE
TYR G:50 , GLY G:51 , ASP G:102 , GLY G:103 , THR G:104 , LYS G:105 , THR G:106 , GLY G:417 , GLY G:418 , ILE G:487 , LEU G:489 , VAL G:502 , GLU G:504 , LYS G:509 , MG G:801
BINDING SITE FOR RESIDUE ATP G 800
14
BC5
SOFTWARE
ASP G:102 , ATP G:800
BINDING SITE FOR RESIDUE MG G 801
15
BC6
SOFTWARE
PRO H:52 , ASP H:102 , GLY H:103 , THR H:104 , LYS H:105 , THR H:106 , GLY H:418 , LEU H:489 , GLU H:504 , LYS H:509 , MG H:801
BINDING SITE FOR RESIDUE ATP H 800
16
BC7
SOFTWARE
ASP H:102 , ATP H:800
BINDING SITE FOR RESIDUE MG H 801
17
BC8
SOFTWARE
TYR I:50 , GLY I:51 , ASP I:102 , GLY I:103 , THR I:104 , LYS I:105 , THR I:106 , SER I:171 , GLY I:418 , ILE I:487 , LEU I:489 , TYR I:490 , GLU I:504 , LYS I:509 , MG I:801
BINDING SITE FOR RESIDUE ATP I 800
18
BC9
SOFTWARE
ASP I:102 , ATP I:800
BINDING SITE FOR RESIDUE MG I 801
19
CC1
SOFTWARE
TYR K:50 , ASP K:102 , GLY K:103 , THR K:104 , LYS K:105 , THR K:106 , GLY K:417 , GLY K:418 , ILE K:487 , LEU K:489 , GLU K:504 , LYS K:509 , MG K:801
BINDING SITE FOR RESIDUE ATP K 800
20
CC2
SOFTWARE
ASP K:102 , ATP K:800
BINDING SITE FOR RESIDUE MG K 801
21
CC3
SOFTWARE
TYR L:50 , PRO L:52 , ASP L:102 , GLY L:103 , THR L:104 , LYS L:105 , THR L:106 , GLY L:417 , GLY L:418 , LEU L:458 , ILE L:487 , LEU L:489 , GLU L:504 , LYS L:509 , MG L:801
BINDING SITE FOR RESIDUE ATP L 800
22
CC4
SOFTWARE
ASP L:102 , ATP L:800
BINDING SITE FOR RESIDUE MG L 801
23
CC5
SOFTWARE
TYR M:50 , GLY M:51 , PRO M:52 , ASP M:102 , GLY M:103 , THR M:104 , LYS M:105 , THR M:106 , GLY M:418 , ILE M:487 , LEU M:489 , GLU M:504 , LYS M:509 , MG M:801
BINDING SITE FOR RESIDUE ATP M 800
24
CC6
SOFTWARE
ASP M:102 , ATP M:800
BINDING SITE FOR RESIDUE MG M 801
25
CC7
SOFTWARE
TYR N:50 , GLY N:51 , PRO N:52 , ASP N:102 , GLY N:103 , THR N:104 , LYS N:105 , THR N:106 , GLY N:417 , GLY N:418 , ILE N:487 , LEU N:489 , GLU N:504 , MG N:801
BINDING SITE FOR RESIDUE ATP N 800
26
CC8
SOFTWARE
ASP N:102 , ATP N:800
BINDING SITE FOR RESIDUE MG N 801
27
CC9
SOFTWARE
TYR O:50 , PRO O:52 , ASP O:102 , GLY O:103 , THR O:104 , LYS O:105 , THR O:106 , GLY O:418 , ILE O:487 , LEU O:489 , GLU O:504 , MG O:801
BINDING SITE FOR RESIDUE ATP O 800
28
DC1
SOFTWARE
ASP O:102 , ATP O:800
BINDING SITE FOR RESIDUE MG O 801
29
DC2
SOFTWARE
TYR P:50 , GLY P:51 , ASP P:102 , GLY P:103 , THR P:104 , LYS P:105 , THR P:106 , GLY P:417 , GLY P:418 , ILE P:487 , LEU P:489 , MET P:497 , GLU P:504 , LYS P:509 , MG P:801
BINDING SITE FOR RESIDUE ATP P 800
30
DC3
SOFTWARE
ASP P:102 , ATP P:800
BINDING SITE FOR RESIDUE MG P 801
31
DC4
SOFTWARE
TYR Q:50 , PRO Q:52 , ASP Q:102 , GLY Q:103 , THR Q:104 , LYS Q:105 , THR Q:106 , GLY Q:418 , ILE Q:487 , TYR Q:490 , MET Q:497 , GLU Q:504 , LYS Q:509 , MG Q:801
BINDING SITE FOR RESIDUE ATP Q 800
32
DC5
SOFTWARE
ASP Q:102 , ATP Q:800
BINDING SITE FOR RESIDUE MG Q 801
33
DC6
SOFTWARE
TYR R:50 , GLY R:51 , PRO R:52 , ASP R:102 , GLY R:103 , THR R:104 , LYS R:105 , THR R:106 , GLY R:417 , GLY R:418 , ILE R:487 , LEU R:489 , MET R:497 , GLU R:504 , LYS R:509 , MG R:801
BINDING SITE FOR RESIDUE ATP R 800
34
DC7
SOFTWARE
ASP R:102 , ATP R:800
BINDING SITE FOR RESIDUE MG R 801
35
DC8
SOFTWARE
TYR S:50 , GLY S:51 , ASP S:102 , GLY S:103 , THR S:104 , LYS S:105 , THR S:106 , SER S:171 , GLY S:418 , VAL S:502 , GLU S:504 , LYS S:509 , MG S:801
BINDING SITE FOR RESIDUE ATP S 800
36
DC9
SOFTWARE
ASP S:102 , ATP S:800
BINDING SITE FOR RESIDUE MG S 801
[
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 K
Chain L
Chain M
Chain N
Chain O
Chain P
Chain Q
Chain R
Chain S
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 (1.2 MB)
Header - Asym.Unit
Biol.Unit 1 (1.2 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
3J1F
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help