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.
3PC8
Asym. Unit
Info
Asym.Unit (133 KB)
Biol.Unit 1 (127 KB)
Biol.Unit 2 (65 KB)
Biol.Unit 3 (64 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY CRYSTAL STRUCTURE OF THE HETERODIMERIC COMPLEX OF XRCC1 AND DNA LIGASE III-ALPHA BRCT DOMAINS.
Authors
:
M. J. Cuneo, J. M. Krahn, R. E. London
Date
:
21 Oct 10 (Deposition) - 15 Jun 11 (Release) - 02 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.31
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,C (1x)
Biol. Unit 3: B,D (1x)
Keywords
:
Dna Repair, Brct Domain, Protein:Protein Interactions, Dna Binding Protein - Ligase Complex, Dna Binding Protein-Ligase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. J. Cuneo, S. A. Gabel, J. M. Krahn, M. A. Ricker, R. E. London
The Structural Basis For Partitioning Of The Xrcc1/Dna Ligase Iii-{Alpha} Brct-Mediated Dimer Complexes.
Nucleic Acids Res. V. 39 7816 2011
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
2a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
1
Ligand/Ion
MAGNESIUM ION
2
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH B:72 , HOH B:170 , HOH B:171 , HOH B:172 , HOH B:215 , HIS B:545
BINDING SITE FOR RESIDUE MG B 1
2
AC2
SOFTWARE
ASP B:555 , ARG B:558 , GLN C:902 , HOH D:25 , HOH D:27 , HOH D:147 , HOH D:155 , HOH D:156 , HOH D:225 , ASP D:876 , ASP D:878
BINDING SITE FOR RESIDUE TRS D 2
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020197 (P899S, chain C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020197
P
986
S
DNLI3_HUMAN
Polymorphism
4986973
C/D
P
899
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: BRCT (-|A:536-627,B:536-627,C:846-921,D:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BRCT
PS50172
BRCT domain profile.
XRCC1_MOUSE
315-403
536-627
2
-
A:536-627
B:536-627
DNLI3_HUMAN
933-1009
2
C:846-921
D:846-921
[
close PROSITE info
]
Exons
(2, 3)
Info
All Exons
Exon 1.17a (- | D:845-845)
Exon 1.17d (C:846-922 | D:846-922)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.16/1.17a
2: Boundary 1.17a/1.17d
3: Boundary 1.17d/-
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
ENST00000378526
1a
ENSE00001429066
chr17:
33307542-33307641
100
DNLI3_HUMAN
-
0
0
-
-
1.2
ENST00000378526
2
ENSE00002172590
chr17:
33310021-33310571
551
DNLI3_HUMAN
1-183
183
0
-
-
1.3
ENST00000378526
3
ENSE00000903608
chr17:
33313007-33313150
144
DNLI3_HUMAN
183-231
49
0
-
-
1.4a
ENST00000378526
4a
ENSE00001106043
chr17:
33316485-33316682
198
DNLI3_HUMAN
231-297
67
0
-
-
1.5
ENST00000378526
5
ENSE00001160722
chr17:
33317982-33318133
152
DNLI3_HUMAN
297-347
51
0
-
-
1.6
ENST00000378526
6
ENSE00001106042
chr17:
33318690-33318856
167
DNLI3_HUMAN
348-403
56
0
-
-
1.7
ENST00000378526
7
ENSE00001106051
chr17:
33318977-33319054
78
DNLI3_HUMAN
403-429
27
0
-
-
1.8
ENST00000378526
8
ENSE00001106059
chr17:
33319543-33319711
169
DNLI3_HUMAN
429-485
57
0
-
-
1.9
ENST00000378526
9
ENSE00001106065
chr17:
33321295-33321450
156
DNLI3_HUMAN
486-537
52
0
-
-
1.10
ENST00000378526
10
ENSE00000713847
chr17:
33323083-33323214
132
DNLI3_HUMAN
538-581
44
0
-
-
1.11
ENST00000378526
11
ENSE00000887588
chr17:
33323593-33323672
80
DNLI3_HUMAN
582-608
27
0
-
-
1.12b
ENST00000378526
12b
ENSE00000343039
chr17:
33324757-33324844
88
DNLI3_HUMAN
608-637
30
0
-
-
1.12c
ENST00000378526
12c
ENSE00000343040
chr17:
33325238-33325315
78
DNLI3_HUMAN
638-663
26
0
-
-
1.13a
ENST00000378526
13a
ENSE00000713843
chr17:
33325623-33325746
124
DNLI3_HUMAN
664-705
42
0
-
-
1.13c
ENST00000378526
13c
ENSE00000887592
chr17:
33326326-33326468
143
DNLI3_HUMAN
705-752
48
0
-
-
1.14
ENST00000378526
14
ENSE00000887593
chr17:
33326801-33326875
75
DNLI3_HUMAN
753-777
25
0
-
-
1.15
ENST00000378526
15
ENSE00000887594
chr17:
33328276-33328422
147
DNLI3_HUMAN
778-826
49
0
-
-
1.16
ENST00000378526
16
ENSE00000343045
chr17:
33328928-33329123
196
DNLI3_HUMAN
827-892
66
0
-
-
1.17a
ENST00000378526
17a
ENSE00000713836
chr17:
33329687-33329808
122
DNLI3_HUMAN
892-932
41
1
-
D:845-845
-
1
1.17d
ENST00000378526
17d
ENSE00001160861
chr17:
33331292-33332083
792
DNLI3_HUMAN
933-1009
77
2
C:846-922
D:846-922
77
77
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3pc8c_ (C:)
1b: SCOP_d3pc8d_ (D:)
2a: SCOP_d3pc8a_ (A:)
2b: SCOP_d3pc8b_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
BRCT domain
(29)
Superfamily
:
BRCT domain
(29)
Family
:
DNA ligase
(6)
Protein domain
:
automated matches
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d3pc8c_
C:
1b
d3pc8d_
D:
Family
:
DNA-repair protein XRCC1
(4)
Protein domain
:
automated matches
(3)
Mouse (Mus musculus) [TaxId: 10090]
(3)
2a
d3pc8a_
A:
2b
d3pc8b_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_BRCT_3pc8B01 (B:536-614)
1b: PFAM_BRCT_3pc8B02 (B:536-614)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
BRCT-like
(38)
Family
:
BRCT
(35)
Mus musculus (Mouse)
(3)
1a
BRCT-3pc8B01
B:536-614
1b
BRCT-3pc8B02
B:536-614
[
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 (133 KB)
Header - Asym.Unit
Biol.Unit 1 (127 KB)
Header - Biol.Unit 1
Biol.Unit 2 (65 KB)
Header - Biol.Unit 2
Biol.Unit 3 (64 KB)
Header - Biol.Unit 3
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
3PC8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help