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.
1K78
Asym. Unit
Info
Asym.Unit (146 KB)
Biol.Unit 1 (77 KB)
Biol.Unit 2 (65 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PAX5(1-149)+ETS-1(331-440)+DNA
Authors
:
C. W. Garvie, J. Hagman, C. Wolberger
Date
:
18 Oct 01 (Deposition) - 04 Jan 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I
Biol. Unit 1: A,B,C,D,I (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Paired Domain, Ets Domain, Transcription Factor, Transcription/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. W. Garvie, J. Hagman, C. Wolberger
Structural Studies Of Ets-1/Pax5 Complex Formation On Dna.
Mol. Cell V. 8 1267 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(9, 19)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_070672 (G24R, chain A/E, )
2: VAR_070673 (V26G, chain A/E, )
3: VAR_070674 (P34Q, chain A/E, )
4: VAR_070675 (D53V, chain A/E, )
5: VAR_070676 (R59G, chain A/E, )
6: VAR_070677 (S66N, chain A/E, )
7: VAR_070678 (T75R, chain A/E, )
8: VAR_070679 (P80R, chain A/E, )
9: VAR_070680 (I139T, chain A/E/I, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_070672
G
24
R
PAX5_HUMAN
Polymorphism
---
A/E
G
24
R
2
UniProt
VAR_070673
V
26
G
PAX5_HUMAN
Polymorphism
---
A/E
V
26
G
3
UniProt
VAR_070674
P
34
Q
PAX5_HUMAN
Polymorphism
---
A/E
P
34
Q
4
UniProt
VAR_070675
D
53
V
PAX5_HUMAN
Polymorphism
---
A/E
D
53
V
5
UniProt
VAR_070676
R
59
G
PAX5_HUMAN
Polymorphism
---
A/E
R
59
G
6
UniProt
VAR_070677
S
66
N
PAX5_HUMAN
Polymorphism
---
A/E
S
66
N
7
UniProt
VAR_070678
T
75
R
PAX5_HUMAN
Polymorphism
---
A/E
T
75
R
8
UniProt
VAR_070679
P
80
R
PAX5_HUMAN
Polymorphism
---
A/E
P
80
R
9
UniProt
VAR_070680
I
139
T
PAX5_HUMAN
Polymorphism
---
A/E/I
I
139
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 8)
Info
All PROSITE Patterns/Profiles
1: PAIRED_1 (A:50-66,E:50-66)
2: ETS_DOMAIN_3 (B:335-415,F:335-415)
3: ETS_DOMAIN_1 (B:337-345,F:337-345)
4: ETS_DOMAIN_2 (B:381-396,F:381-396)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PAIRED_1
PS00034
Paired domain signature.
PAX5_HUMAN
50-66
2
A:50-66
E:50-66
2
ETS_DOMAIN_3
PS50061
Ets-domain profile.
ETS1_MOUSE
335-415
2
B:335-415
F:335-415
3
ETS_DOMAIN_1
PS00345
Ets-domain signature 1.
ETS1_MOUSE
337-345
2
B:337-345
F:337-345
4
ETS_DOMAIN_2
PS00346
Ets-domain signature 2.
ETS1_MOUSE
381-396
2
B:381-396
F:381-396
[
close PROSITE info
]
Exons
(3, 8)
Info
All Exons
Exon 1.3 (A:19-71 | E:19-71 | -)
Exon 1.4 (A:71-137 | E:71-137 | I:84-137)
Exon 1.5 (A:137-142 | E:137-142 | I:137-141)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1a/1.3
2: Boundary 1.3/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6b
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
1.1a
ENST00000358127
1a
ENSE00001927054
chr9:
37034103-37033983
121
PAX5_HUMAN
1-16
16
0
-
-
1.3
ENST00000358127
3
ENSE00001700848
chr9:
37020798-37020633
166
PAX5_HUMAN
16-71
56
2
A:19-71
E:19-71
-
53
53
-
1.4
ENST00000358127
4
ENSE00001800669
chr9:
37015191-37014994
198
PAX5_HUMAN
71-137
67
3
A:71-137
E:71-137
I:84-137
67
67
54
1.5
ENST00000358127
5
ENSE00001662228
chr9:
37006534-37006470
65
PAX5_HUMAN
137-159
23
3
A:137-142
E:137-142
I:137-141
6
6
5
1.6b
ENST00000358127
6b
ENSE00001148776
chr9:
37002773-37002645
129
PAX5_HUMAN
159-202
44
0
-
-
1.7a
ENST00000358127
7a
ENSE00001148771
chr9:
36966721-36966546
176
PAX5_HUMAN
202-260
59
0
-
-
1.11a
ENST00000358127
11a
ENSE00000928305
chr9:
36923481-36923352
130
PAX5_HUMAN
261-304
44
0
-
-
1.12
ENST00000358127
12
ENSE00001636100
chr9:
36882102-36882001
102
PAX5_HUMAN
304-338
35
0
-
-
1.13
ENST00000358127
13
ENSE00001754297
chr9:
36846926-36846840
87
PAX5_HUMAN
338-367
30
0
-
-
1.14d
ENST00000358127
14d
ENSE00001860138
chr9:
36840633-36833272
7362
PAX5_HUMAN
367-391
25
0
-
-
[
close EXON info
]
SCOP Domains
(2, 7)
Info
All SCOP Domains
1a: SCOP_d1k78a1 (A:19-81)
1b: SCOP_d1k78a2 (A:82-142)
1c: SCOP_d1k78e1 (E:19-81)
1d: SCOP_d1k78e2 (E:82-142)
1e: SCOP_d1k78i1 (I:84-141)
2a: SCOP_d1k78b_ (B:)
2b: SCOP_d1k78f_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Homeodomain-like
(373)
Family
:
Paired domain
(4)
Protein domain
:
Pax-5
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1k78a1
A:19-81
1b
d1k78a2
A:82-142
1c
d1k78e1
E:19-81
1d
d1k78e2
E:82-142
1e
d1k78i1
I:84-141
Superfamily
:
Winged helix DNA-binding domain
(576)
Family
:
ets domain
(23)
Protein domain
:
ETS-1 transcription factor, residues 331-440
(9)
Mouse (Mus musculus) [TaxId: 10090]
(6)
2a
d1k78b_
B:
2b
d1k78f_
F:
[
close SCOP info
]
CATH Domains
(1, 7)
Info
all CATH domains
1a: CATH_1k78A01 (A:19-84)
1b: CATH_1k78E01 (E:19-84)
1c: CATH_1k78B00 (B:335-436)
1d: CATH_1k78F00 (F:334-436)
1e: CATH_1k78I00 (I:84-141)
1f: CATH_1k78A02 (A:85-139)
1g: CATH_1k78E02 (E:85-138)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
'winged helix' repressor DNA binding domain
(507)
[unclassified]
(77)
1a
1k78A01
A:19-84
1b
1k78E01
E:19-84
1c
1k78B00
B:335-436
1d
1k78F00
F:334-436
1e
1k78I00
I:84-141
1f
1k78A02
A:85-139
1g
1k78E02
E:85-138
[
close CATH info
]
Pfam Domains
(2, 5)
Info
all PFAM domains
1a: PFAM_Ets_1k78F01 (F:334-417)
1b: PFAM_Ets_1k78F02 (F:334-417)
2a: PFAM_PAX_1k78I01 (I:84-140)
2b: PFAM_PAX_1k78I02 (I:84-140)
2c: PFAM_PAX_1k78I03 (I:84-140)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HTH
(544)
Family
:
Ets
(14)
Mus musculus (Mouse)
(8)
1a
Ets-1k78F01
F:334-417
1b
Ets-1k78F02
F:334-417
Family
:
PAX
(4)
Homo sapiens (Human)
(3)
2a
PAX-1k78I01
I:84-140
2b
PAX-1k78I02
I:84-140
2c
PAX-1k78I03
I:84-140
[
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
Chain G
Chain H
Chain I
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 (146 KB)
Header - Asym.Unit
Biol.Unit 1 (77 KB)
Header - Biol.Unit 1
Biol.Unit 2 (65 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
1K78
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help