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.
5JQG
Asym. Unit
Info
Asym.Unit (745 KB)
Biol.Unit 1 (731 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
AN APO TUBULIN-RB-TTL COMPLEX STRUCTURE USED FOR SIDE-BY-SIDE COMPARISON
Authors
:
Y. X. Wang, J. H. Naismith, X. Zhu
Date
:
04 May 16 (Deposition) - 18 May 16 (Release) - 18 May 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.24
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Apo Structure, Structural Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. X. Wang, J. H. Naismith
An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison
To Be Published
[
close entry info
]
Hetero Components
(7, 15)
Info
All Hetero Components
1a: PHOSPHOMETHYLPHOSPHONIC ACID ADENY... (ACPa)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
3a: CHLORIDE ION (CLa)
4a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
5a: GUANOSINE-5'-TRIPHOSPHATE (GTPa)
5b: GUANOSINE-5'-TRIPHOSPHATE (GTPb)
5c: GUANOSINE-5'-TRIPHOSPHATE (GTPc)
6a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
6b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
7a: MAGNESIUM ION (MGa)
7b: MAGNESIUM ION (MGb)
7c: MAGNESIUM ION (MGc)
7d: MAGNESIUM ION (MGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACP
1
Ligand/Ion
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2
CA
3
Ligand/Ion
CALCIUM ION
3
CL
1
Ligand/Ion
CHLORIDE ION
4
GDP
1
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
5
GTP
3
Ligand/Ion
GUANOSINE-5'-TRIPHOSPHATE
6
MES
2
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
7
MG
4
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(15, 15)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:10 , GLN A:11 , ALA A:12 , GLN A:15 , ASP A:98 , ALA A:99 , ALA A:100 , ASN A:101 , SER A:140 , GLY A:143 , GLY A:144 , THR A:145 , GLY A:146 , VAL A:177 , THR A:179 , GLU A:183 , ASN A:206 , TYR A:224 , ASN A:228 , ILE A:231 , MG A:502 , HOH A:609 , HOH A:615 , HOH A:616 , HOH A:633 , HOH A:643 , HOH A:645 , HOH A:647 , LYS B:252
binding site for residue GTP A 501
02
AC2
SOFTWARE
GTP A:501 , HOH A:616 , HOH A:633 , HOH A:645 , HOH A:647
binding site for residue MG A 502
03
AC3
SOFTWARE
ASP A:39 , THR A:41 , GLY A:44 , GLU A:55 , HOH A:603
binding site for residue CA A 503
04
AC4
SOFTWARE
TYR A:161 , GLY A:162 , LYS A:163 , LYS A:164
binding site for residue CL A 504
05
AC5
SOFTWARE
GLY B:10 , GLN B:11 , CYS B:12 , GLN B:15 , SER B:138 , GLY B:141 , GLY B:142 , THR B:143 , GLY B:144 , PRO B:171 , VAL B:175 , ASP B:177 , GLU B:181 , ASN B:204 , TYR B:222 , ASN B:226 , MG B:502 , HOH B:601 , HOH B:606 , HOH B:609 , HOH B:612 , HOH B:623 , HOH B:631 , HOH B:643 , HOH B:653
binding site for residue GDP B 501
06
AC6
SOFTWARE
GLN B:11 , GDP B:501 , HOH B:602 , HOH B:643 , HOH B:653 , HOH C:627
binding site for residue MG B 502
07
AC7
SOFTWARE
GLU B:111
binding site for residue CA B 503
08
AC8
SOFTWARE
TRP A:407 , ARG B:156 , PRO B:160 , ASP B:161 , ARG B:162 , ASN B:195 , ASP B:197 , ARG B:251
binding site for residue MES B 504
09
AC9
SOFTWARE
PHE B:294 , ASP B:295 , ALA B:296 , ASP B:304 , ARG B:306 , ASN B:337 , HOH B:608
binding site for residue MES B 505
10
AD1
SOFTWARE
GLY C:10 , GLN C:11 , ALA C:12 , GLN C:15 , ASP C:98 , ALA C:99 , ALA C:100 , ASN C:101 , SER C:140 , GLY C:143 , GLY C:144 , THR C:145 , GLY C:146 , VAL C:177 , GLU C:183 , ASN C:206 , TYR C:224 , ASN C:228 , ILE C:231 , MG C:502 , HOH C:607 , HOH C:610 , HOH C:633 , HOH C:644 , HOH C:645 , HOH C:676 , HOH C:692 , LYS D:252
binding site for residue GTP C 501
11
AD2
SOFTWARE
GTP C:501 , HOH C:607 , HOH C:633 , HOH C:645 , HOH C:692
binding site for residue MG C 502
12
AD3
SOFTWARE
ASP C:39 , THR C:41 , GLY C:44 , GLU C:55 , HOH C:615
binding site for residue CA C 503
13
AD4
SOFTWARE
GLY D:10 , GLN D:11 , CYS D:12 , GLN D:15 , ALA D:97 , GLY D:98 , ASN D:99 , SER D:138 , GLY D:141 , GLY D:142 , THR D:143 , GLY D:144 , GLU D:181 , ASN D:204 , TYR D:222 , ASN D:226 , MG D:502 , HOH D:601 , HOH D:605 , HOH D:607 , HOH D:613 , HOH D:622
binding site for residue GTP D 501
14
AD5
SOFTWARE
GTP D:501 , HOH D:601 , HOH D:605 , HOH D:629
binding site for residue MG D 502
15
AD6
SOFTWARE
LYS F:74 , ILE F:148 , LYS F:150 , GLN F:183 , LYS F:184 , TYR F:185 , LEU F:186 , LYS F:198 , ASP F:200 , ARG F:202 , ARG F:222 , THR F:241 , ASN F:242 , ASP F:318 , ILE F:330 , GLU F:331 , ASN F:333
binding site for residue ACP F 401
[
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
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 (745 KB)
Header - Asym.Unit
Biol.Unit 1 (731 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
5JQG
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
