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.
4AB3
Asym. Unit
Info
Asym.Unit (944 KB)
Biol.Unit 1 (930 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ATP-TRIGGERED MOLECULAR MECHANICS OF THE CHAPERONIN GROEL
Authors
:
D. K. Clare, D. Vasishtan, S. Stagg, J. Quispe, G. W. Farr, M. Topf, A. L. H H. R. Saibil
Date
:
06 Dec 11 (Deposition) - 12 Dec 12 (Release) - 25 Sep 13 (Revision)
Method
:
ELECTRON MICROSCOPY
Resolution
:
8.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N (1x)
Keywords
:
Chaperone
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. K. Clare, D. Vasishtan, S. Stagg, J. Quispe, G. W. Farr, M. Topf, A. L. Horwich, H. R. Saibil
Atp-Triggered Conformational Changes Delineate Substrate-Binding And -Folding Mechanics Of The Groel Chaperonin.
Cell(Cambridge, Mass. ) V. 149 113 2012
[
close entry info
]
Hetero Components
(3, 42)
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)
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)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
3e: PHOSPHATE ION (PO4e)
3f: PHOSPHATE ION (PO4f)
3g: PHOSPHATE ION (PO4g)
3h: PHOSPHATE ION (PO4h)
3i: PHOSPHATE ION (PO4i)
3j: PHOSPHATE ION (PO4j)
3k: PHOSPHATE ION (PO4k)
3l: PHOSPHATE ION (PO4l)
3m: PHOSPHATE ION (PO4m)
3n: PHOSPHATE ION (PO4n)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
14
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
MG
14
Ligand/Ion
MAGNESIUM ION
3
PO4
14
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(42, 42)
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)
42: EC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:51 , ASP A:52 , ATP A:1527
BINDING SITE FOR RESIDUE PO4 A1525
02
AC2
SOFTWARE
ASP A:87 , GLY A:88 , SER A:151 , ATP A:1527
BINDING SITE FOR RESIDUE MG A1526
03
AC3
SOFTWARE
LEU A:31 , GLY A:53 , ASP A:87 , GLY A:88 , THR A:89 , THR A:90 , THR A:91 , ILE A:150 , ASN A:153 , GLY A:414 , GLY A:415 , ILE A:454 , ASP A:495 , PO4 A:1525 , MG A:1526
BINDING SITE FOR RESIDUE ATP A1527
04
AC4
SOFTWARE
LYS B:51 , ASP B:52 , ATP B:1527
BINDING SITE FOR RESIDUE PO4 B1525
05
AC5
SOFTWARE
ASP B:87 , GLY B:88 , SER B:151 , ATP B:1527
BINDING SITE FOR RESIDUE MG B1526
06
AC6
SOFTWARE
LEU B:31 , GLY B:53 , ASP B:87 , GLY B:88 , THR B:89 , THR B:90 , THR B:91 , ILE B:150 , SER B:151 , ASN B:153 , GLY B:414 , GLY B:415 , ILE B:454 , ASP B:495 , PO4 B:1525 , MG B:1526
BINDING SITE FOR RESIDUE ATP B1527
07
AC7
SOFTWARE
LYS C:51 , ASP C:52 , ATP C:1527
BINDING SITE FOR RESIDUE PO4 C1525
08
AC8
SOFTWARE
ASP C:87 , GLY C:88 , SER C:151 , ATP C:1527
BINDING SITE FOR RESIDUE MG C1526
09
AC9
SOFTWARE
LEU C:31 , GLY C:53 , ASP C:87 , GLY C:88 , THR C:89 , THR C:90 , THR C:91 , ILE C:150 , ASN C:153 , GLY C:414 , GLY C:415 , ILE C:454 , ASP C:495 , PO4 C:1525 , MG C:1526
BINDING SITE FOR RESIDUE ATP C1527
10
BC1
SOFTWARE
ASP D:52 , ATP D:1527
BINDING SITE FOR RESIDUE PO4 D1525
11
BC2
SOFTWARE
ASP D:87 , GLY D:88 , SER D:151 , ATP D:1527
BINDING SITE FOR RESIDUE MG D1526
12
BC3
SOFTWARE
LEU D:31 , GLY D:53 , ASP D:87 , GLY D:88 , THR D:89 , THR D:90 , THR D:91 , ILE D:150 , ASN D:153 , GLY D:414 , GLY D:415 , ILE D:454 , ASP D:495 , PO4 D:1525 , MG D:1526
BINDING SITE FOR RESIDUE ATP D1527
13
BC4
SOFTWARE
LYS E:51 , ASP E:52 , ATP E:1527
BINDING SITE FOR RESIDUE PO4 E1525
14
BC5
SOFTWARE
ASP E:87 , GLY E:88 , SER E:151 , ATP E:1527
BINDING SITE FOR RESIDUE MG E1526
15
BC6
SOFTWARE
LEU E:31 , GLY E:53 , ASP E:87 , GLY E:88 , THR E:89 , THR E:90 , THR E:91 , ILE E:150 , ASN E:153 , GLY E:414 , GLY E:415 , ILE E:454 , ASP E:495 , PO4 E:1525 , MG E:1526
BINDING SITE FOR RESIDUE ATP E1527
16
BC7
SOFTWARE
ASP F:52 , ATP F:1527
BINDING SITE FOR RESIDUE PO4 F1525
17
BC8
SOFTWARE
ASP F:87 , GLY F:88 , SER F:151 , ATP F:1527
BINDING SITE FOR RESIDUE MG F1526
18
BC9
SOFTWARE
LEU F:31 , GLY F:53 , ASP F:87 , GLY F:88 , THR F:89 , THR F:90 , THR F:91 , ILE F:150 , ASN F:153 , GLY F:414 , GLY F:415 , ILE F:454 , ASP F:495 , PO4 F:1525 , MG F:1526
BINDING SITE FOR RESIDUE ATP F1527
19
CC1
SOFTWARE
LYS G:51 , ASP G:52 , ATP G:1527
BINDING SITE FOR RESIDUE PO4 G1525
20
CC2
SOFTWARE
ASP G:87 , GLY G:88 , SER G:151 , ATP G:1527
BINDING SITE FOR RESIDUE MG G1526
21
CC3
SOFTWARE
LEU G:31 , GLY G:53 , ASP G:87 , GLY G:88 , THR G:89 , THR G:90 , THR G:91 , ILE G:150 , ASN G:153 , GLY G:414 , GLY G:415 , ILE G:454 , ASP G:495 , PO4 G:1525 , MG G:1526
BINDING SITE FOR RESIDUE ATP G1527
22
CC4
SOFTWARE
ASP H:52 , ASN H:153 , MG H:1526 , ATP H:1527
BINDING SITE FOR RESIDUE PO4 H1525
23
CC5
SOFTWARE
ASP H:87 , GLY H:88 , PO4 H:1525 , ATP H:1527
BINDING SITE FOR RESIDUE MG H1526
24
CC6
SOFTWARE
LEU H:31 , ASP H:52 , GLY H:53 , ASP H:87 , GLY H:88 , THR H:89 , THR H:90 , THR H:91 , ASN H:153 , GLY H:414 , GLY H:415 , ILE H:454 , TYR H:478 , ASN H:479 , ALA H:480 , ALA H:481 , ILE H:493 , ASP H:495 , PO4 H:1525 , MG H:1526
BINDING SITE FOR RESIDUE ATP H1527
25
CC7
SOFTWARE
ASP I:52 , ASN I:153 , MG I:1526 , ATP I:1527
BINDING SITE FOR RESIDUE PO4 I1525
26
CC8
SOFTWARE
ASP I:87 , GLY I:88 , PO4 I:1525 , ATP I:1527
BINDING SITE FOR RESIDUE MG I1526
27
CC9
SOFTWARE
LEU I:31 , ASP I:52 , GLY I:53 , ASP I:87 , GLY I:88 , THR I:89 , THR I:90 , THR I:91 , ASN I:153 , GLY I:414 , GLY I:415 , ILE I:454 , TYR I:478 , ASN I:479 , ALA I:480 , ALA I:481 , ILE I:493 , ASP I:495 , PO4 I:1525 , MG I:1526
BINDING SITE FOR RESIDUE ATP I1527
28
DC1
SOFTWARE
ASP J:52 , ASN J:153 , MG J:1526 , ATP J:1527
BINDING SITE FOR RESIDUE PO4 J1525
29
DC2
SOFTWARE
ASP J:87 , GLY J:88 , PO4 J:1525 , ATP J:1527
BINDING SITE FOR RESIDUE MG J1526
30
DC3
SOFTWARE
LEU J:31 , ASP J:52 , GLY J:53 , ASP J:87 , GLY J:88 , THR J:89 , THR J:90 , THR J:91 , ASN J:153 , GLY J:414 , GLY J:415 , ILE J:454 , TYR J:478 , ASN J:479 , ALA J:480 , ALA J:481 , ILE J:493 , ASP J:495 , PO4 J:1525 , MG J:1526
BINDING SITE FOR RESIDUE ATP J1527
31
DC4
SOFTWARE
ASP K:52 , ASN K:153 , MG K:1526 , ATP K:1527
BINDING SITE FOR RESIDUE PO4 K1525
32
DC5
SOFTWARE
ASP K:87 , GLY K:88 , PO4 K:1525 , ATP K:1527
BINDING SITE FOR RESIDUE MG K1526
33
DC6
SOFTWARE
LEU K:31 , ASP K:52 , GLY K:53 , ASP K:87 , GLY K:88 , THR K:89 , THR K:90 , THR K:91 , ASN K:153 , GLY K:414 , GLY K:415 , ILE K:454 , TYR K:478 , ASN K:479 , ALA K:480 , ALA K:481 , ILE K:493 , ASP K:495 , PO4 K:1525 , MG K:1526
BINDING SITE FOR RESIDUE ATP K1527
34
DC7
SOFTWARE
ASP L:52 , ASN L:153 , MG L:1526 , ATP L:1527
BINDING SITE FOR RESIDUE PO4 L1525
35
DC8
SOFTWARE
ASP L:87 , GLY L:88 , PO4 L:1525 , ATP L:1527
BINDING SITE FOR RESIDUE MG L1526
36
DC9
SOFTWARE
LEU L:31 , ASP L:52 , GLY L:53 , ASP L:87 , GLY L:88 , THR L:89 , THR L:90 , THR L:91 , ASN L:153 , GLY L:414 , GLY L:415 , ILE L:454 , TYR L:478 , ASN L:479 , ALA L:480 , ALA L:481 , ILE L:493 , ASP L:495 , PO4 L:1525 , MG L:1526
BINDING SITE FOR RESIDUE ATP L1527
37
EC1
SOFTWARE
ASP M:52 , ASN M:153 , MG M:1526 , ATP M:1527
BINDING SITE FOR RESIDUE PO4 M1525
38
EC2
SOFTWARE
ASP M:87 , GLY M:88 , PO4 M:1525 , ATP M:1527
BINDING SITE FOR RESIDUE MG M1526
39
EC3
SOFTWARE
LEU M:31 , ASP M:52 , GLY M:53 , ASP M:87 , GLY M:88 , THR M:89 , THR M:90 , THR M:91 , ASN M:153 , GLY M:414 , GLY M:415 , ILE M:454 , TYR M:478 , ASN M:479 , ALA M:480 , ALA M:481 , ILE M:493 , ASP M:495 , PO4 M:1525 , MG M:1526
BINDING SITE FOR RESIDUE ATP M1527
40
EC4
SOFTWARE
ASP N:52 , ASN N:153 , MG N:1526 , ATP N:1527
BINDING SITE FOR RESIDUE PO4 N1525
41
EC5
SOFTWARE
ASP N:87 , GLY N:88 , PO4 N:1525 , ATP N:1527
BINDING SITE FOR RESIDUE MG N1526
42
EC6
SOFTWARE
LEU N:31 , ASP N:52 , GLY N:53 , ASP N:87 , GLY N:88 , THR N:89 , THR N:90 , THR N:91 , ASN N:153 , GLY N:414 , GLY N:415 , ILE N:454 , TYR N:478 , ASN N:479 , ALA N:480 , ALA N:481 , ILE N:493 , ASP N:495 , PO4 N:1525 , MG N:1526
BINDING SITE FOR RESIDUE ATP N1527
[
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, 14)
Info
All PROSITE Patterns/Profiles
1: CHAPERONINS_CPN60 (A:405-416,B:405-416,C:405-416,D:40...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CHAPERONINS_CPN60
PS00296
Chaperonins cpn60 signature.
CH60_ECOLI
405-416
14
A:405-416
B:405-416
C:405-416
D:405-416
E:405-416
F:405-416
G:405-416
H:405-416
I:405-416
J:405-416
K:405-416
L:405-416
M:405-416
N:405-416
[
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
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 (944 KB)
Header - Asym.Unit
Biol.Unit 1 (930 KB)
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
4AB3
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help