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.
4JNE
Asym. Unit
Info
Asym.Unit (419 KB)
Biol.Unit 1 (407 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ALLOSTERIC OPENING OF THE POLYPEPTIDE-BINDING SITE WHEN AN HSP70 BINDS ATP
Authors
:
R. Qi, E. B. Sarbeng, Q. Liu, K. Q. Le, X. Xu, H. Xu, J. Yang, J. L. Wong, C. Vo W. A. Hendrickson, L. Zhou, Q. Liu
Date
:
15 Mar 13 (Deposition) - 29 May 13 (Release) - 07 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.96
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Dnak, Chaperone, 70Kda Heat Shock Protein (Hsp70), Atp-Binding, Nucleotide Binding Domain (Nbd), Substructure Binding Domain (Sbd), Allosteric Coupling
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Qi, E. B. Sarbeng, Q. Liu, K. Q. Le, X. Xu, H. Xu, J. Yang, J. L. Wong, C. Vorvis, W. A. Hendrickson, L. Zhou, Q. Liu
Allosteric Opening Of The Polypeptide-Binding Site When An Hsp70 Binds Atp.
Nat. Struct. Mol. Biol. V. 20 900 2013
[
close entry info
]
Hetero Components
(4, 19)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
GOL
4
Ligand/Ion
GLYCEROL
3
MG
2
Ligand/Ion
MAGNESIUM ION
4
SO4
11
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ATP A:1002 , HOH A:1101 , HOH A:1102 , HOH A:1104 , HOH A:1520
BINDING SITE FOR RESIDUE MG A 1001
02
AC2
SOFTWARE
GLY A:10 , THR A:11 , THR A:12 , ASN A:13 , LYS A:70 , GLY A:196 , GLY A:197 , GLY A:198 , ALA A:199 , GLY A:229 , GLU A:267 , LYS A:270 , ILE A:271 , SER A:274 , GLY A:341 , GLY A:342 , GLN A:343 , ARG A:345 , MG A:1001 , HOH A:1101 , HOH A:1102 , HOH A:1104 , HOH A:1106 , HOH A:1109 , HOH A:1116 , HOH A:1121 , HOH A:1176 , HOH A:1184 , HOH A:1254 , HOH A:1520 , HOH B:1197
BINDING SITE FOR RESIDUE ATP A 1002
03
AC3
SOFTWARE
ARG A:25 , ARG A:34 , GOL A:1008 , HOH A:1166 , HOH A:1344 , HOH A:1555 , HOH A:1709 , ASN B:366
BINDING SITE FOR RESIDUE SO4 A 1003
04
AC4
SOFTWARE
ARG A:445 , LYS A:446 , HOH A:1192 , HOH A:1684
BINDING SITE FOR RESIDUE SO4 A 1004
05
AC5
SOFTWARE
ARG A:188 , ARG A:362 , HOH A:1569
BINDING SITE FOR RESIDUE SO4 A 1005
06
AC6
SOFTWARE
SER A:427 , MET A:428 , GLY A:429 , GLY A:430 , HOH A:1492 , MET B:428 , SO4 B:1006
BINDING SITE FOR RESIDUE SO4 A 1006
07
AC7
SOFTWARE
ARG A:467 , HIS A:544 , SER A:545 , LYS A:548 , HOH A:1518 , HOH A:1775 , VAL B:407 , ARG B:447
BINDING SITE FOR RESIDUE SO4 A 1007
08
AC8
SOFTWARE
ARG A:25 , VAL A:26 , LEU A:27 , GLU A:28 , ARG A:34 , SO4 A:1003 , HOH A:1144 , ASN B:366
BINDING SITE FOR RESIDUE GOL A 1008
09
AC9
SOFTWARE
ARG A:84 , ARG A:235 , ARG A:315
BINDING SITE FOR RESIDUE GOL A 1009
10
BC1
SOFTWARE
ATP B:1002 , HOH B:1101 , HOH B:1102 , HOH B:1376 , HOH B:1491
BINDING SITE FOR RESIDUE MG B 1001
11
BC2
SOFTWARE
HOH A:1149 , GLY B:10 , THR B:11 , THR B:12 , ASN B:13 , LYS B:70 , GLY B:196 , GLY B:197 , GLY B:198 , ALA B:199 , GLY B:229 , GLU B:267 , LYS B:270 , ILE B:271 , SER B:274 , GLY B:341 , GLY B:342 , GLN B:343 , ARG B:345 , MG B:1001 , HOH B:1101 , HOH B:1102 , HOH B:1105 , HOH B:1109 , HOH B:1111 , HOH B:1121 , HOH B:1136 , HOH B:1140 , HOH B:1192 , HOH B:1376 , HOH B:1491
BINDING SITE FOR RESIDUE ATP B 1002
12
BC3
SOFTWARE
ASN A:366 , ARG B:25 , ARG B:34 , GOL B:1009 , HOH B:1200 , HOH B:1427 , HOH B:1457 , HOH B:1625 , HOH B:1809
BINDING SITE FOR RESIDUE SO4 B 1003
13
BC4
SOFTWARE
LYS A:268 , ARG B:56 , HOH B:1524 , HOH B:1669
BINDING SITE FOR RESIDUE SO4 B 1004
14
BC5
SOFTWARE
ARG B:188 , ARG B:362 , HOH B:1623
BINDING SITE FOR RESIDUE SO4 B 1005
15
BC6
SOFTWARE
MET A:428 , SO4 A:1006 , SER B:427 , MET B:428 , GLY B:429 , GLY B:430 , HOH B:1808
BINDING SITE FOR RESIDUE SO4 B 1006
16
BC7
SOFTWARE
VAL A:407 , ARG A:447 , ARG B:467 , SER B:545 , LYS B:548 , HOH B:1605
BINDING SITE FOR RESIDUE SO4 B 1007
17
BC8
SOFTWARE
HOH A:1481 , HOH A:1518 , ARG B:445 , LYS B:446 , ARG B:447 , HOH B:1166
BINDING SITE FOR RESIDUE SO4 B 1008
18
BC9
SOFTWARE
ASN A:366 , HOH A:1232 , ARG B:25 , VAL B:26 , GLU B:28 , ARG B:34 , TYR B:130 , SO4 B:1003 , HOH B:1168
BINDING SITE FOR RESIDUE GOL B 1009
19
CC1
SOFTWARE
ASP B:231 , ARG B:235 , ARG B:315 , HOH B:1517 , HOH B:1747
BINDING SITE FOR RESIDUE GOL B 1010
[
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
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 (419 KB)
Header - Asym.Unit
Biol.Unit 1 (407 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
4JNE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help