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.
3SVG
Asym. Unit
Info
Asym.Unit (52 KB)
Biol.Unit 1 (48 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 THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH A 3,5-DIMETHYLISOXAZOL LIGAND
Authors
:
P. Filippakopoulos, S. Picaud, I. Felletar, S. D. Hewings, F. Von Delf C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, S. J. Conway, S Structural Genomics Consortium (Sgc)
Date
:
12 Jul 11 (Deposition) - 10 Aug 11 (Release) - 10 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.68
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Isoxazole, Bromodomain, Structural Genomics, Structural Genomics Consortium, Sgc, Unknown Function
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Filippakopoulos, S. Picaud, I. Felletar, S. D. Hewings, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, S. J. Conway, S. Knapp
Crystal Structure Of The First Bromodomain Of Human Brd4 In Complex With A 3, 5-Dimethylisoxazol Ligand
To Be Published
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
2a: (1R)-1-[3-(3,5-DIMETHYL-1,2-OXAZOL... (ODRa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
2
ODR
1
Ligand/Ion
(1R)-1-[3-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-5-ETHOXYPHENYL]ETHANOL
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ILE A:100 , ILE A:101 , LYS A:102 , THR A:103 , ASN A:135
BINDING SITE FOR RESIDUE EDO A 1
2
AC2
SOFTWARE
TYR A:137 , ILE A:138 , GLN A:159 , LYS A:160 , GLU A:163 , HOH A:238
BINDING SITE FOR RESIDUE EDO A 2
3
AC3
SOFTWARE
VAL A:69 , TYR A:137 , ASN A:140 , LYS A:141 , PRO A:142 , VAL A:147 , LYS A:160 , HOH A:239 , HOH A:253
BINDING SITE FOR RESIDUE EDO A 3
4
AC4
SOFTWARE
HOH A:7 , HOH A:18 , HOH A:23 , TRP A:81 , PRO A:82 , GLN A:85 , ASP A:96 , LYS A:99 , ASN A:140 , ILE A:146 , MET A:149
BINDING SITE FOR RESIDUE ODR A 169
[
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
(2, 2)
Info
All PROSITE Patterns/Profiles
1: BROMODOMAIN_2 (A:75-147|-)
2: BROMODOMAIN_1 (A:80-139)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BROMODOMAIN_2
PS50014
Bromodomain profile.
BRD4_HUMAN
75-147
368-440
1
A:75-147
-
2
BROMODOMAIN_1
PS00633
Bromodomain signature.
BRD4_HUMAN
80-139
1
A:80-139
[
close PROSITE info
]
Exons
(3, 3)
Info
All Exons
Exon 1.2 (A:42-95)
Exon 1.3 (A:96-141)
Exon 1.4 (A:142-168)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
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
1.1
ENST00000263377
1
ENSE00001113198
chr19:
15391262-15391075
188
BRD4_HUMAN
-
0
0
-
-
1.2
ENST00000263377
2
ENSE00001113202
chr19:
15383944-15383626
319
BRD4_HUMAN
1-95
95
1
A:42-95
54
1.3
ENST00000263377
3
ENSE00000689046
chr19:
15379853-15379716
138
BRD4_HUMAN
96-141
46
1
A:96-141
46
1.4
ENST00000263377
4
ENSE00000689047
chr19:
15378362-15378227
136
BRD4_HUMAN
142-187
46
1
A:142-168
27
1.5
ENST00000263377
5
ENSE00000689048
chr19:
15376454-15376165
290
BRD4_HUMAN
187-283
97
0
-
-
1.6
ENST00000263377
6
ENSE00000348853
chr19:
15375577-15375215
363
BRD4_HUMAN
284-404
121
0
-
-
1.7
ENST00000263377
7
ENSE00000689050
chr19:
15374359-15374231
129
BRD4_HUMAN
405-447
43
0
-
-
1.8
ENST00000263377
8
ENSE00000689051
chr19:
15367984-15367775
210
BRD4_HUMAN
448-517
70
0
-
-
1.9
ENST00000263377
9
ENSE00000689052
chr19:
15367074-15366875
200
BRD4_HUMAN
518-584
67
0
-
-
1.10
ENST00000263377
10
ENSE00000689053
chr19:
15366403-15366108
296
BRD4_HUMAN
584-683
100
0
-
-
1.11
ENST00000263377
11
ENSE00001187704
chr19:
15365073-15364963
111
BRD4_HUMAN
683-720
38
0
-
-
1.15
ENST00000263377
15
ENSE00001113203
chr19:
15355573-15355521
53
BRD4_HUMAN
720-737
18
0
-
-
1.16
ENST00000263377
16
ENSE00001055985
chr19:
15355411-15355042
370
BRD4_HUMAN
738-861
124
0
-
-
1.17
ENST00000263377
17
ENSE00001055976
chr19:
15354298-15353711
588
BRD4_HUMAN
861-1057
197
0
-
-
1.18
ENST00000263377
18
ENSE00001136676
chr19:
15350833-15350721
113
BRD4_HUMAN
1057-1094
38
0
-
-
1.19
ENST00000263377
19
ENSE00001113200
chr19:
15350632-15350470
163
BRD4_HUMAN
1095-1149
55
0
-
-
1.20
ENST00000263377
20
ENSE00001113199
chr19:
15350333-15350203
131
BRD4_HUMAN
1149-1192
44
0
-
-
1.21
ENST00000263377
21
ENSE00000951121
chr19:
15350075-15349870
206
BRD4_HUMAN
1193-1261
69
0
-
-
1.22
ENST00000263377
22
ENSE00000951122
chr19:
15349791-15349554
238
BRD4_HUMAN
1261-1340
80
0
-
-
1.23
ENST00000263377
23
ENSE00001055981
chr19:
15349256-15348301
956
BRD4_HUMAN
1341-1362
22
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3svga_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Bromodomain
(203)
Family
:
automated matches
(169)
Protein domain
:
automated matches
(169)
Human (Homo sapiens) [TaxId: 9606]
(162)
1a
d3svga_
A:
[
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
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 (52 KB)
Header - Asym.Unit
Biol.Unit 1 (48 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
3SVG
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
