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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4BD8
Asym. Unit
Info
Asym.Unit (202 KB)
Biol.Unit 1 (103 KB)
Biol.Unit 2 (95 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
BAX DOMAIN SWAPPED DIMER INDUCED BY BIMBH3 WITH CHAPS
Authors
:
P. E. Czabotar, D. Westphal, J. M. Adams, P. M. Colman
Date
:
05 Oct 12 (Deposition) - 13 Feb 13 (Release) - 13 Feb 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.22
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Apoptosis, Programmed Cell Death
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. E. Czabotar, D. Westphal, G. Dewson, S. Ma, C. Hockings, W. D. Fairlie, E. F. Lee, S. Yao, A. Y. Robin, B. J. Smith, D. C. Huang, R. M. Kluck, J. M. Adams, P. M. Colman
Bax Crystal Structures Reveal How Bh3 Domains Activate Bax And Nucleate Its Oligomerization To Induce Apoptosis.
Cell(Cambridge, Mass. ) V. 152 519 2013
[
close entry info
]
Hetero Components
(2, 10)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
2a: PRASEODYMIUM ION (PRa)
2b: PRASEODYMIUM ION (PRb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
8
Ligand/Ion
1,2-ETHANEDIOL
2
PR
2
Ligand/Ion
PRASEODYMIUM ION
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:142 , GLU A:146 , HOH A:2069 , GLU B:69 , ASP C:142 , GLU C:146
BINDING SITE FOR RESIDUE PR A1171
02
AC2
SOFTWARE
ASP B:142 , GLU B:146 , ASP D:142 , GLU D:146 , HOH D:2034
BINDING SITE FOR RESIDUE PR B1171
03
AC3
SOFTWARE
ASN A:73 , MET A:74 , GLU A:75 , HOH A:2037
BINDING SITE FOR RESIDUE EDO A1172
04
AC4
SOFTWARE
SER C:16 , GLN C:18 , GLN D:153 , GLY D:157
BINDING SITE FOR RESIDUE EDO D1171
05
AC5
SOFTWARE
THR A:169 , ASN B:106 , ARG B:109
BINDING SITE FOR RESIDUE EDO A1173
06
AC6
SOFTWARE
SER A:16 , HOH A:2005 , GLN B:153
BINDING SITE FOR RESIDUE EDO A1174
07
AC7
SOFTWARE
SER A:87 , PRO A:88 , ARG A:89 , GLU A:90
BINDING SITE FOR RESIDUE EDO A1175
08
AC8
SOFTWARE
GLU A:131 , ARG A:134 , THR A:135 , GLU B:75 , HOH B:2025
BINDING SITE FOR RESIDUE EDO A1176
09
AC9
SOFTWARE
GLN B:52 , ASP B:53 , HOH C:2014
BINDING SITE FOR RESIDUE EDO B1172
10
BC1
SOFTWARE
GLN B:52
BINDING SITE FOR RESIDUE EDO B1173
[
close Site info
]
SAPs(SNPs)/Variants
(3, 9)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_013575 (G11E, chain A, )
2: VAR_007809 (G67R, chain A/B/C/D, )
3: VAR_013576 (G108V, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_013575
G
11
E
BAX_HUMAN
Unclassified
---
A
G
11
E
2
UniProt
VAR_007809
G
67
R
BAX_HUMAN
Unclassified
---
A/B/C/D
G
67
R
3
UniProt
VAR_013576
G
108
V
BAX_HUMAN
Unclassified
---
A/B/C/D
G
108
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 16)
Info
All PROSITE Patterns/Profiles
1: BH3 (A:59-73,B:59-73,C:59-73,D:59-73)
2: BCL2_FAMILY (A:63-160,B:63-160,C:63-160,D:63-16...)
3: BH1 (A:99-118,B:99-118,C:99-118,D:99-11...)
4: BH2 (A:151-162,B:151-162,C:151-162,D:15...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BH3
PS01259
Apoptosis regulator, Bcl-2 family BH3 motif signature.
BAX_HUMAN
59-73
4
A:59-73
B:59-73
C:59-73
D:59-73
2
BCL2_FAMILY
PS50062
BCL2-like apoptosis inhibitors family profile.
BAX_HUMAN
63-160
4
A:63-160
B:63-160
C:63-160
D:63-160
3
BH1
PS01080
Apoptosis regulator, Bcl-2 family BH1 motif signature.
BAX_HUMAN
99-118
4
A:99-118
B:99-118
C:99-118
D:99-118
4
BH2
PS01258
Apoptosis regulator, Bcl-2 family BH2 motif signature.
BAX_HUMAN
151-162
4
A:151-162
B:151-162
C:151-162
D:151-162
[
close PROSITE info
]
Exons
(6, 22)
Info
All Exons
Exon 1.1b (A:11-12 | B:12-12 | - | -)
Exon 1.1f (A:12-29 | B:12-29 | C:16-29 | D:14...)
Exon 1.1h (A:29-78 (gaps) | B:29-78 (gaps) | ...)
Exon 1.2c (A:78-123 | B:78-123 | C:78-123 (ga...)
Exon 1.4b (A:124-158 | B:124-158 | C:124-158 ...)
Exon 1.4m (A:159-170 | B:159-170 | C:159-170 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1b
2: Boundary 1.1b/1.1f
3: Boundary 1.1f/1.1h
4: Boundary 1.1h/1.2c
5: Boundary 1.2c/1.4b
6: Boundary 1.4b/1.4m
7: Boundary 1.4m/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1b
ENST00000345358
1b
ENSE00001558844
chr19:
49458134-49458219
86
BAX_HUMAN
1-12
12
2
A:11-12
B:12-12
-
-
2
1
-
-
1.1f
ENST00000345358
1f
ENSE00000853382
chr19:
49458805-49458856
52
BAX_HUMAN
12-29
18
4
A:12-29
B:12-29
C:16-29
D:14-29
18
18
14
16
1.1h
ENST00000345358
1h
ENSE00001704034
chr19:
49458944-49459090
147
BAX_HUMAN
29-78
50
4
A:29-78 (gaps)
B:29-78 (gaps)
C:29-78 (gaps)
D:29-78 (gaps)
50
50
50
50
1.2c
ENST00000345358
2c
ENSE00001678231
chr19:
49459455-49459590
136
BAX_HUMAN
78-123
46
4
A:78-123
B:78-123
C:78-123 (gaps)
D:78-123 (gaps)
46
46
46
46
1.4b
ENST00000345358
4b
ENSE00001654505
chr19:
49464067-49464171
105
BAX_HUMAN
124-158
35
4
A:124-158
B:124-158
C:124-158
D:124-158
35
35
35
35
1.4m
ENST00000345358
4m
ENSE00001636776
chr19:
49464789-49465055
267
BAX_HUMAN
159-192
34
4
A:159-170
B:159-170
C:159-170
D:159-170
12
12
12
12
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d4bd8a_ (A:)
1b: SCOP_d4bd8b_ (B:)
1c: SCOP_d4bd8c_ (C:)
1d: SCOP_d4bd8d_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Toxins' membrane translocation domains
(135)
Superfamily
:
Bcl-2 inhibitors of programmed cell death
(113)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d4bd8a_
A:
1b
d4bd8b_
B:
1c
d4bd8c_
C:
1d
d4bd8d_
D:
[
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
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 (202 KB)
Header - Asym.Unit
Biol.Unit 1 (103 KB)
Header - Biol.Unit 1
Biol.Unit 2 (95 KB)
Header - Biol.Unit 2
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
4BD8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help