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.
4DL5
Asym. Unit
Info
Asym.Unit (88 KB)
Biol.Unit 1 (83 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN DNA POLYMERASE ETA INSERTING DCMPNPP OPPOSITE THE 5'G OF CISPLATIN CROSSLINKED GS (PT-GG2).
Authors
:
Y. Zhao, C. Biertumpfel, M. Gregory, F. Hanaoka, Y. Hua, W. Yang
Date
:
05 Feb 12 (Deposition) - 09 May 12 (Release) - 08 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.92
Chains
:
Asym. Unit : A,P,T
Biol. Unit 1: A,P,T (1x)
Keywords
:
Cisplatin, Chemoresistence, Translesion Synthesis, Human Dna Polymerse Eta, Kinetics, Molecular Splint, Inhibition, Dna Distorsion, Second Tls Polymerase, Nucleotidyl Transfer Reaction, Pcna, Transferase-Dna-Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Zhao, C. Biertumpfel, M. T. Gregory, Y. J. Hua, F. Hanaoka, W. Yang
Structural Basis For Chemoresistance To Cisplatin Mediated By Dna Polymerase Eta
Proc. Natl. Acad. Sci. Usa V. 109 7269 2012
[
close entry info
]
Hetero Components
(3, 4)
Info
All Hetero Components
1a: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HY... (0KXa)
2a: CISPLATIN (CPTa)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0KX
1
Ligand/Ion
2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
2
CPT
1
Ligand/Ion
CISPLATIN
3
MG
2
Ligand/Ion
MAGNESIUM ION
[
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
ASP A:13 , MET A:14 , ASP A:115 , MG A:502 , 0KX A:503 , DC P:9
BINDING SITE FOR RESIDUE MG A 501
2
AC2
SOFTWARE
ASP A:13 , SER A:113 , ASP A:115 , GLU A:116 , MG A:501 , 0KX A:503 , DA P:8 , DC P:9
BINDING SITE FOR RESIDUE MG A 502
3
AC3
SOFTWARE
ASP A:13 , MET A:14 , ASP A:15 , CYS A:16 , PHE A:17 , PHE A:18 , ILE A:48 , ALA A:49 , TYR A:52 , ARG A:55 , ARG A:61 , ASP A:115 , LYS A:231 , MG A:501 , MG A:502 , DA P:8 , DC P:9 , DG T:4 , DG T:5
BINDING SITE FOR RESIDUE 0KX A 503
4
AC4
SOFTWARE
DA P:8 , DG T:4 , DG T:5 , DT T:6 , DC T:7
BINDING SITE FOR RESIDUE CPT T 101
[
close Site info
]
SAPs(SNPs)/Variants
(10, 10)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_070836 (R93P, chain A, )
02: VAR_021227 (R111H, chain A, )
03: VAR_021228 (T122P, chain A, )
04: VAR_036220 (G153D, chain A, )
05: VAR_021229 (G209V, chain A, )
06: VAR_021230 (G263V, chain A, )
07: VAR_070837 (V266D, chain A, )
08: VAR_070838 (G295R, chain A, )
09: VAR_021231 (R334W, chain A, )
10: VAR_021232 (R361S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_070836
R
93
P
POLH_HUMAN
Disease (XPV)
---
A
R
93
P
02
UniProt
VAR_021227
R
111
H
POLH_HUMAN
Disease (XPV)
---
A
R
111
H
03
UniProt
VAR_021228
T
122
P
POLH_HUMAN
Disease (XPV)
---
A
T
122
P
04
UniProt
VAR_036220
G
153
D
POLH_HUMAN
Unclassified
---
A
G
153
D
05
UniProt
VAR_021229
G
209
V
POLH_HUMAN
Polymorphism
2307456
A
G
209
V
06
UniProt
VAR_021230
G
263
V
POLH_HUMAN
Disease (XPV)
---
A
G
263
V
07
UniProt
VAR_070837
V
266
D
POLH_HUMAN
Disease (XPV)
---
A
V
266
D
08
UniProt
VAR_070838
G
295
R
POLH_HUMAN
Disease (XPV)
---
A
G
295
R
09
UniProt
VAR_021231
R
334
W
POLH_HUMAN
Polymorphism
9333548
A
R
334
W
10
UniProt
VAR_021232
R
361
S
POLH_HUMAN
Disease (XPV)
---
A
R
361
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: UMUC (A:9-259)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UMUC
PS50173
UmuC domain profile.
POLH_HUMAN
9-259
1
A:9-259
[
close PROSITE info
]
Exons
(10, 10)
Info
All Exons
Exon 1.2 (A:2-46)
Exon 1.3 (A:46-91)
Exon 1.4b (A:91-164 (gaps))
Exon 1.5 (A:164-220)
Exon 1.6 (A:221-255)
Exon 1.7 (A:255-295)
Exon 1.8 (A:295-336)
Exon 1.9 (A:337-358)
Exon 1.10 (A:359-415 (gaps))
Exon 1.11a (A:415-432)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4b
04: Boundary 1.4b/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11a
11: Boundary 1.11a/-
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
ENST00000372236
1a
ENSE00001717994
chr6:
43543887-43544177
291
POLH_HUMAN
-
0
0
-
-
1.2
ENST00000372236
2
ENSE00001457304
chr6:
43550053-43550193
141
POLH_HUMAN
1-46
46
1
A:2-46
45
1.3
ENST00000372236
3
ENSE00002161294
chr6:
43550744-43550878
135
POLH_HUMAN
46-91
46
1
A:46-91
46
1.4b
ENST00000372236
4b
ENSE00000752927
chr6:
43555009-43555226
218
POLH_HUMAN
91-164
74
1
A:91-164 (gaps)
74
1.5
ENST00000372236
5
ENSE00000481500
chr6:
43565433-43565602
170
POLH_HUMAN
164-220
57
1
A:164-220
57
1.6
ENST00000372236
6
ENSE00001172213
chr6:
43568725-43568828
104
POLH_HUMAN
221-255
35
1
A:221-255
35
1.7
ENST00000372236
7
ENSE00001172207
chr6:
43571629-43571748
120
POLH_HUMAN
255-295
41
1
A:255-295
41
1.8
ENST00000372236
8
ENSE00001172201
chr6:
43572352-43572475
124
POLH_HUMAN
295-336
42
1
A:295-336
42
1.9
ENST00000372236
9
ENSE00001172195
chr6:
43572991-43573056
66
POLH_HUMAN
337-358
22
1
A:337-358
22
1.10
ENST00000372236
10
ENSE00001172191
chr6:
43578291-43578460
170
POLH_HUMAN
359-415
57
1
A:359-415 (gaps)
57
1.11a
ENST00000372236
11a
ENSE00001861041
chr6:
43581397-43583397
2001
POLH_HUMAN
415-713
299
1
A:415-432
18
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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 P
Chain T
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 (88 KB)
Header - Asym.Unit
Biol.Unit 1 (83 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
4DL5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help