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.
5XDO
Asym. Unit
Info
Asym.Unit (182 KB)
Biol.Unit 1 (175 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN VOLTAGE-DEPENDENT ANION CHANNEL 1 (HVDAC1) IN C222 SPACE GROUP
Authors
:
T. Hosaka, T. Kimura-Someya, M. Shirouzu
Date
:
28 Mar 17 (Deposition) - 28 Jun 17 (Release) - 28 Jun 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Membrane Protein, Cell-Free Synthesis, Beta-Barrel Structure
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Hosaka, M. Okazaki, T. Kimura-Someya, Y. Ishizuka-Katsura, K. Ito S. Yokoyama, K. Dodo, M. Sodeoka, M. Shirouzu
Crystal Structural Characterization Reveals Novel Oligomeri Interactions Of Human Voltage-Dependent Anion Channel 1
Protein Sci. 2017
[
close entry info
]
Hetero Components
(4, 9)
Info
All Hetero Components
1a: HEXANE (HEXa)
2a: PENTANE (LNKa)
2b: PENTANE (LNKb)
3a: N-OCTANE (OCTa)
3b: N-OCTANE (OCTb)
3c: N-OCTANE (OCTc)
3d: N-OCTANE (OCTd)
4a: SPERMIDINE (SPDa)
4b: SPERMIDINE (SPDb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEX
1
Ligand/Ion
HEXANE
2
LNK
2
Ligand/Ion
PENTANE
3
OCT
4
Ligand/Ion
N-OCTANE
4
SPD
2
Ligand/Ion
SPERMIDINE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:7 , LEU A:10 , GLN A:154 , ASN A:183
binding site for residue SPD A 301
2
AC2
SOFTWARE
ASN A:214 , PHE B:219 , OCT B:302
binding site for residue OCT A 302
3
AC3
SOFTWARE
SER A:167 , PHE A:169
binding site for residue OCT A 303
4
AC4
SOFTWARE
TYR A:153
binding site for residue LNK A 304
5
AC5
SOFTWARE
ARG A:120
binding site for residue HEX A 306
6
AC6
SOFTWARE
TYR B:7 , LEU B:10 , ARG B:15 , HIS B:181 , THR B:182 , ASN B:183
binding site for residue SPD B 301
7
AC7
SOFTWARE
LEU A:208 , OCT A:302
binding site for residue OCT B 302
8
AC8
SOFTWARE
PHE B:190 , TRP B:210 , GLY B:213
binding site for residue OCT B 303
[
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 (182 KB)
Header - Asym.Unit
Biol.Unit 1 (175 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
5XDO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help