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.
2B2U
Asym. Unit
Info
Asym.Unit (79 KB)
Biol.Unit 1 (73 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
TANDEM CHROMODOMAINS OF HUMAN CHD1 COMPLEXED WITH HISTONE H3 TAIL CONTAINING TRIMETHYLLYSINE 4 AND DIMETHYLARGININE 2
Authors
:
J. F. Flanagan Iv, L. -Z. Mi, M. Chruszcz, M. Cymborowski, K. L. Clines, W. Minor, F. Rastinejad, S. Khorasanizadeh
Date
:
19 Sep 05 (Deposition) - 27 Dec 05 (Release) - 06 Nov 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.95
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Chd, Chromodomain, Three Stranded Antiparallel Beta Sheet, Alpha Helix Linker, Histone H3, Asymmetric Dimethylarginine, Trimethyllysine, Peptide Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. F. Flanagan, L. Z. Mi, M. Chruszcz, M. Cymborowski, K. L. Clines, Y. Kim, W. Minor, F. Rastinejad, S. Khorasanizadeh
Double Chromodomains Cooperate To Recognize The Methylated Histone H3 Tail.
Nature V. 438 1181 2005
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: NG,NG-DIMETHYL-L-ARGININE (DA2a)
2a: N-TRIMETHYLLYSINE (M3La)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DA2
1
Mod. Amino Acid
NG,NG-DIMETHYL-L-ARGININE
2
M3L
1
Mod. Amino Acid
N-TRIMETHYLLYSINE
[
close Hetero Component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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, 10)
Info
All PROSITE Patterns/Profiles
1: CHROMO_2 (A:14-106,B:14-106,C:14-99|A:131-18...)
2: CHROMO_1 (A:60-80,B:60-80,C:60-80|A:151-171,...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CHROMO_2
PS50013
Chromo and chromo shadow domain profile.
CHD1_HUMAN
272-364
389-452
5
A:14-106
B:14-106
C:14-99
A:131-185
B:131-185
2
CHROMO_1
PS00598
Chromo domain signature.
CHD1_HUMAN
318-338
409-429
5
A:60-80
B:60-80
C:60-80
A:151-171
B:151-171
[
close PROSITE info
]
Exons
(5, 11)
Info
All Exons
Exon 1.6 (A:13-29 | B:11-29 | C:13-29)
Exon 1.7 (A:29-104 (gaps) | B:29-104 (gaps) ...)
Exon 1.8 (A:104-138 | B:104-138 | -)
Exon 1.9 (A:138-187 | B:138-185 (gaps) | -)
Exon 2.2b (D:1-5)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.5/1.6
2: Boundary 1.6/1.7
3: Boundary 1.7/1.8
4: Boundary 1.8/1.9
5: Boundary 1.9/1.10
6: Boundary -/2.2b
7: Boundary 2.2b/-
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
ENST00000284049
1
ENSE00001083439
chr5:
98262240-98262038
203
CHD1_HUMAN
1-18
18
0
-
-
1.2
ENST00000284049
2
ENSE00001013117
chr5:
98240802-98240601
202
CHD1_HUMAN
18-85
68
0
-
-
1.3
ENST00000284049
3
ENSE00001013104
chr5:
98239612-98239496
117
CHD1_HUMAN
86-124
39
0
-
-
1.4
ENST00000284049
4
ENSE00001013106
chr5:
98238668-98238604
65
CHD1_HUMAN
125-146
22
0
-
-
1.5
ENST00000284049
5
ENSE00001013090
chr5:
98237039-98236890
150
CHD1_HUMAN
146-196
51
0
-
-
1.6
ENST00000284049
6
ENSE00001013110
chr5:
98236786-98236515
272
CHD1_HUMAN
196-287
92
3
A:13-29
B:11-29
C:13-29
17
19
17
1.7
ENST00000284049
7
ENSE00001013103
chr5:
98235409-98235184
226
CHD1_HUMAN
287-362
76
3
A:29-104 (gaps)
B:29-104 (gaps)
C:29-99
76
76
71
1.8
ENST00000284049
8
ENSE00001013118
chr5:
98234468-98234368
101
CHD1_HUMAN
362-396
35
2
A:104-138
B:104-138
-
35
35
-
1.9
ENST00000284049
9
ENSE00001013088
chr5:
98234138-98233960
179
CHD1_HUMAN
396-455
60
2
A:138-187
B:138-185 (gaps)
-
50
48
-
1.10
ENST00000284049
10
ENSE00001013119
chr5:
98233024-98232897
128
CHD1_HUMAN
456-498
43
0
-
-
1.11
ENST00000284049
11
ENSE00001013116
chr5:
98232146-98231930
217
CHD1_HUMAN
498-570
73
0
-
-
1.12
ENST00000284049
12
ENSE00001013097
chr5:
98230390-98230301
90
CHD1_HUMAN
571-600
30
0
-
-
1.13
ENST00000284049
13
ENSE00001013099
chr5:
98229310-98229120
191
CHD1_HUMAN
601-664
64
0
-
-
1.14
ENST00000284049
14
ENSE00001013102
chr5:
98228417-98228229
189
CHD1_HUMAN
664-727
64
0
-
-
1.15
ENST00000284049
15
ENSE00001013109
chr5:
98224942-98224780
163
CHD1_HUMAN
727-781
55
0
-
-
1.16a
ENST00000284049
16a
ENSE00001013120
chr5:
98223944-98223792
153
CHD1_HUMAN
782-832
51
0
-
-
1.17b
ENST00000284049
17b
ENSE00001013095
chr5:
98221353-98221282
72
CHD1_HUMAN
833-856
24
0
-
-
1.18b
ENST00000284049
18b
ENSE00001013089
chr5:
98218941-98218792
150
CHD1_HUMAN
857-906
50
0
-
-
1.19
ENST00000284049
19
ENSE00001013108
chr5:
98217827-98217679
149
CHD1_HUMAN
907-956
50
0
-
-
1.20a
ENST00000284049
20a
ENSE00001013092
chr5:
98217079-98216983
97
CHD1_HUMAN
956-988
33
0
-
-
1.21
ENST00000284049
21
ENSE00001013105
chr5:
98216875-98216780
96
CHD1_HUMAN
989-1020
32
0
-
-
1.22
ENST00000284049
22
ENSE00001013113
chr5:
98215432-98215256
177
CHD1_HUMAN
1021-1079
59
0
-
-
1.23
ENST00000284049
23
ENSE00001013094
chr5:
98212262-98212102
161
CHD1_HUMAN
1080-1133
54
0
-
-
1.24
ENST00000284049
24
ENSE00001013115
chr5:
98210817-98210776
42
CHD1_HUMAN
1133-1147
15
0
-
-
1.25
ENST00000284049
25
ENSE00001013111
chr5:
98209427-98209297
131
CHD1_HUMAN
1147-1191
45
0
-
-
1.26b
ENST00000284049
26b
ENSE00001013091
chr5:
98208259-98208121
139
CHD1_HUMAN
1191-1237
47
0
-
-
1.26c
ENST00000284049
26c
ENSE00001013112
chr5:
98207905-98207755
151
CHD1_HUMAN
1237-1287
51
0
-
-
1.27a
ENST00000284049
27a
ENSE00001013096
chr5:
98206507-98206391
117
CHD1_HUMAN
1288-1326
39
0
-
-
1.28a
ENST00000284049
28a
ENSE00001013086
chr5:
98205586-98205458
129
CHD1_HUMAN
1327-1369
43
0
-
-
1.30a
ENST00000284049
30a
ENSE00001013100
chr5:
98204339-98204199
141
CHD1_HUMAN
1370-1416
47
0
-
-
1.31
ENST00000284049
31
ENSE00001013087
chr5:
98199290-98199112
179
CHD1_HUMAN
1417-1476
60
0
-
-
1.32d
ENST00000284049
32d
ENSE00001013093
chr5:
98195772-98195676
97
CHD1_HUMAN
1476-1508
33
0
-
-
1.33
ENST00000284049
33
ENSE00001013098
chr5:
98194719-98194668
52
CHD1_HUMAN
1509-1526
18
0
-
-
1.34b
ENST00000284049
34b
ENSE00001013114
chr5:
98194094-98193884
211
CHD1_HUMAN
1526-1596
71
0
-
-
1.35d
ENST00000284049
35d
ENSE00002036745
chr5:
98192429-98191449
981
CHD1_HUMAN
1596-1710
115
0
-
-
2.2b
ENST00000359303
2b
ENSE00001974165
chr6:
27858570-27858160
411
H31_HUMAN
1-136
136
1
D:1-5
5
[
close EXON info
]
SCOP Domains
(1, 5)
Info
All SCOP Domains
1a: SCOP_d2b2ua1 (A:108-187)
1b: SCOP_d2b2ua2 (A:13-107)
1c: SCOP_d2b2ub1 (B:108-185)
1d: SCOP_d2b2ub2 (B:13-107)
1e: SCOP_d2b2uc1 (C:13-97)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
SH3-like barrel
(1035)
Superfamily
:
Chromo domain-like
(82)
Family
:
Chromo domain
(41)
Protein domain
:
ATP-dependent helicase CHD1 (Chromo domain protein 1)
(7)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d2b2ua1
A:108-187
1b
d2b2ua2
A:13-107
1c
d2b2ub1
B:108-185
1d
d2b2ub2
B:13-107
1e
d2b2uc1
C:13-97
[
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 (79 KB)
Header - Asym.Unit
Biol.Unit 1 (73 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
2B2U
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help