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.
4GZ0
Biol. Unit 6
Info
Asym.Unit (597 KB)
Biol.Unit 1 (105 KB)
Biol.Unit 2 (105 KB)
Biol.Unit 3 (105 KB)
Biol.Unit 4 (102 KB)
Biol.Unit 5 (103 KB)
Biol.Unit 6 (103 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MUS MUSCULUS TDP2-DNA SUBSTRATE ANALOG (5'-6-AMINOHEXANOL) COMPLEX
Authors
:
M. J. Schellenberg, R. S. Williams
Date
:
05 Sep 12 (Deposition) - 31 Oct 12 (Release) - 02 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.11
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,D (1x)
Biol. Unit 2: B,C (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: I,J (1x)
Biol. Unit 6: K,L (1x)
Keywords
:
Protein-Dna Complex, Dna Repair, 5'-Dna End Processing, Endonuclease/Exonuclease/Phosphatase Domain, Eep Domain, 5'-Dna End Recognition, Eep, Endonuclease/Exonuclease/Phosphatase Domain, 5'-End Recognition, Nuclear, Hydrolase, Hydrolase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. J. Schellenberg, C. D. Appel, S. Adhikari, P. D. Robertson, D. A. Ramsden, R. S. Williams
Mechanism Of Repair Of 5'-Topoisomerase Ii-Dna Adducts By Mammalian Tyrosyl-Dna Phosphodiesterase 2.
Nat. Struct. Mol. Biol. V. 19 1363 2012
[
close entry info
]
Hetero Components
(3, 18)
Info
All Hetero Components
1a: 6-AMINOHEXAN-1-OL (6AHa)
1b: 6-AMINOHEXAN-1-OL (6AHb)
1c: 6-AMINOHEXAN-1-OL (6AHc)
1d: 6-AMINOHEXAN-1-OL (6AHd)
1e: 6-AMINOHEXAN-1-OL (6AHe)
1f: 6-AMINOHEXAN-1-OL (6AHf)
2a: ACETATE ION (ACTa)
2b: ACETATE ION (ACTb)
2c: ACETATE ION (ACTc)
2d: ACETATE ION (ACTd)
2e: ACETATE ION (ACTe)
2f: ACETATE ION (ACTf)
2g: ACETATE ION (ACTg)
2h: ACETATE ION (ACTh)
2i: ACETATE ION (ACTi)
2j: ACETATE ION (ACTj)
2k: ACETATE ION (ACTk)
2l: ACETATE ION (ACTl)
2m: ACETATE ION (ACTm)
2n: ACETATE ION (ACTn)
2o: ACETATE ION (ACTo)
2p: ACETATE ION (ACTp)
2q: ACETATE ION (ACTq)
2r: ACETATE ION (ACTr)
2s: ACETATE ION (ACTs)
2t: ACETATE ION (ACTt)
2u: ACETATE ION (ACTu)
2v: ACETATE ION (ACTv)
3a: 1,2-ETHANEDIOL (EDOa)
3aa: 1,2-ETHANEDIOL (EDOaa)
3ab: 1,2-ETHANEDIOL (EDOab)
3ac: 1,2-ETHANEDIOL (EDOac)
3ad: 1,2-ETHANEDIOL (EDOad)
3ae: 1,2-ETHANEDIOL (EDOae)
3af: 1,2-ETHANEDIOL (EDOaf)
3ag: 1,2-ETHANEDIOL (EDOag)
3ah: 1,2-ETHANEDIOL (EDOah)
3ai: 1,2-ETHANEDIOL (EDOai)
3aj: 1,2-ETHANEDIOL (EDOaj)
3ak: 1,2-ETHANEDIOL (EDOak)
3al: 1,2-ETHANEDIOL (EDOal)
3am: 1,2-ETHANEDIOL (EDOam)
3an: 1,2-ETHANEDIOL (EDOan)
3ao: 1,2-ETHANEDIOL (EDOao)
3ap: 1,2-ETHANEDIOL (EDOap)
3aq: 1,2-ETHANEDIOL (EDOaq)
3ar: 1,2-ETHANEDIOL (EDOar)
3as: 1,2-ETHANEDIOL (EDOas)
3at: 1,2-ETHANEDIOL (EDOat)
3au: 1,2-ETHANEDIOL (EDOau)
3av: 1,2-ETHANEDIOL (EDOav)
3aw: 1,2-ETHANEDIOL (EDOaw)
3ax: 1,2-ETHANEDIOL (EDOax)
3ay: 1,2-ETHANEDIOL (EDOay)
3az: 1,2-ETHANEDIOL (EDOaz)
3b: 1,2-ETHANEDIOL (EDOb)
3ba: 1,2-ETHANEDIOL (EDOba)
3bb: 1,2-ETHANEDIOL (EDObb)
3bc: 1,2-ETHANEDIOL (EDObc)
3bd: 1,2-ETHANEDIOL (EDObd)
3be: 1,2-ETHANEDIOL (EDObe)
3bf: 1,2-ETHANEDIOL (EDObf)
3bg: 1,2-ETHANEDIOL (EDObg)
3bh: 1,2-ETHANEDIOL (EDObh)
3bi: 1,2-ETHANEDIOL (EDObi)
3bj: 1,2-ETHANEDIOL (EDObj)
3bk: 1,2-ETHANEDIOL (EDObk)
3bl: 1,2-ETHANEDIOL (EDObl)
3bm: 1,2-ETHANEDIOL (EDObm)
3bn: 1,2-ETHANEDIOL (EDObn)
3bo: 1,2-ETHANEDIOL (EDObo)
3bp: 1,2-ETHANEDIOL (EDObp)
3bq: 1,2-ETHANEDIOL (EDObq)
3br: 1,2-ETHANEDIOL (EDObr)
3bs: 1,2-ETHANEDIOL (EDObs)
3bt: 1,2-ETHANEDIOL (EDObt)
3bu: 1,2-ETHANEDIOL (EDObu)
3bv: 1,2-ETHANEDIOL (EDObv)
3bw: 1,2-ETHANEDIOL (EDObw)
3bx: 1,2-ETHANEDIOL (EDObx)
3by: 1,2-ETHANEDIOL (EDOby)
3bz: 1,2-ETHANEDIOL (EDObz)
3c: 1,2-ETHANEDIOL (EDOc)
3ca: 1,2-ETHANEDIOL (EDOca)
3cb: 1,2-ETHANEDIOL (EDOcb)
3cc: 1,2-ETHANEDIOL (EDOcc)
3cd: 1,2-ETHANEDIOL (EDOcd)
3ce: 1,2-ETHANEDIOL (EDOce)
3cf: 1,2-ETHANEDIOL (EDOcf)
3cg: 1,2-ETHANEDIOL (EDOcg)
3ch: 1,2-ETHANEDIOL (EDOch)
3ci: 1,2-ETHANEDIOL (EDOci)
3cj: 1,2-ETHANEDIOL (EDOcj)
3ck: 1,2-ETHANEDIOL (EDOck)
3cl: 1,2-ETHANEDIOL (EDOcl)
3cm: 1,2-ETHANEDIOL (EDOcm)
3cn: 1,2-ETHANEDIOL (EDOcn)
3co: 1,2-ETHANEDIOL (EDOco)
3cp: 1,2-ETHANEDIOL (EDOcp)
3cq: 1,2-ETHANEDIOL (EDOcq)
3cr: 1,2-ETHANEDIOL (EDOcr)
3cs: 1,2-ETHANEDIOL (EDOcs)
3ct: 1,2-ETHANEDIOL (EDOct)
3cu: 1,2-ETHANEDIOL (EDOcu)
3cv: 1,2-ETHANEDIOL (EDOcv)
3cw: 1,2-ETHANEDIOL (EDOcw)
3cx: 1,2-ETHANEDIOL (EDOcx)
3cy: 1,2-ETHANEDIOL (EDOcy)
3cz: 1,2-ETHANEDIOL (EDOcz)
3d: 1,2-ETHANEDIOL (EDOd)
3da: 1,2-ETHANEDIOL (EDOda)
3db: 1,2-ETHANEDIOL (EDOdb)
3dc: 1,2-ETHANEDIOL (EDOdc)
3dd: 1,2-ETHANEDIOL (EDOdd)
3de: 1,2-ETHANEDIOL (EDOde)
3df: 1,2-ETHANEDIOL (EDOdf)
3dg: 1,2-ETHANEDIOL (EDOdg)
3dh: 1,2-ETHANEDIOL (EDOdh)
3di: 1,2-ETHANEDIOL (EDOdi)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
3y: 1,2-ETHANEDIOL (EDOy)
3z: 1,2-ETHANEDIOL (EDOz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6AH
1
Ligand/Ion
6-AMINOHEXAN-1-OL
2
ACT
3
Ligand/Ion
ACETATE ION
3
EDO
14
Ligand/Ion
1,2-ETHANEDIOL
[
close Hetero Component info
]
Sites
(24, 24)
Info
All Sites
01: GC4 (SOFTWARE)
02: GC8 (SOFTWARE)
03: GC9 (SOFTWARE)
04: HC6 (SOFTWARE)
05: IC5 (SOFTWARE)
06: IC8 (SOFTWARE)
07: JC1 (SOFTWARE)
08: JC2 (SOFTWARE)
09: JC3 (SOFTWARE)
10: JC4 (SOFTWARE)
11: JC5 (SOFTWARE)
12: JC6 (SOFTWARE)
13: JC7 (SOFTWARE)
14: JC8 (SOFTWARE)
15: JC9 (SOFTWARE)
16: KC1 (SOFTWARE)
17: KC2 (SOFTWARE)
18: KC3 (SOFTWARE)
19: KC4 (SOFTWARE)
20: KC5 (SOFTWARE)
21: KC6 (SOFTWARE)
22: KC7 (SOFTWARE)
23: KC8 (SOFTWARE)
24: KC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
GC4
SOFTWARE
TYR E:153 , ASP E:343 , HOH E:664 , CYS K:149 , LEU K:152 , GLU K:348 , EDO K:412
BINDING SITE FOR RESIDUE EDO E 403
02
GC8
SOFTWARE
SER E:148 , ALA E:151 , SER K:341 , HOH K:528 , HOH K:579
BINDING SITE FOR RESIDUE EDO E 407
03
GC9
SOFTWARE
ACT E:422 , EDO K:403
BINDING SITE FOR RESIDUE EDO E 408
04
HC6
SOFTWARE
CYS E:149 , TYR E:153 , VAL E:345 , GLY E:346 , LEU E:347 , EDO K:409 , EDO K:412
BINDING SITE FOR RESIDUE EDO E 414
05
IC5
SOFTWARE
SER E:125 , TYR E:153 , EDO E:408 , LEU K:152
BINDING SITE FOR RESIDUE ACT E 422
06
IC8
SOFTWARE
GLU E:162 , SER E:239 , DC F:2 , DG F:4 , DT L:8
BINDING SITE FOR RESIDUE 6AH F 101
07
JC1
SOFTWARE
TRP K:307 , ASP K:308 , THR K:309 , ASN K:312 , ASN K:314 , LEU K:315 , ASP K:358
BINDING SITE FOR RESIDUE EDO K 401
08
JC2
SOFTWARE
ARG E:144 , GLY E:145 , SER E:148 , GLU E:348 , HIS K:302 , ASP K:343 , HOH K:514 , HOH K:579
BINDING SITE FOR RESIDUE EDO K 402
09
JC3
SOFTWARE
SER E:341 , EDO E:408 , HOH E:617 , SER K:148 , ALA K:151
BINDING SITE FOR RESIDUE EDO K 403
10
JC4
SOFTWARE
HIS E:302 , ARG K:144 , GLY K:145 , SER K:148 , HOH K:519
BINDING SITE FOR RESIDUE EDO K 404
11
JC5
SOFTWARE
LEU E:347 , GLU E:348 , LYS E:349 , ALA K:311 , EDO K:408 , HOH K:516
BINDING SITE FOR RESIDUE EDO K 405
12
JC6
SOFTWARE
TYR K:153 , SER K:154
BINDING SITE FOR RESIDUE EDO K 406
13
JC7
SOFTWARE
LEU K:139 , TYR K:170
BINDING SITE FOR RESIDUE EDO K 407
14
JC8
SOFTWARE
TYR K:305 , ASP K:308 , ALA K:311 , LEU K:344 , TRP K:360 , EDO K:405
BINDING SITE FOR RESIDUE EDO K 408
15
JC9
SOFTWARE
CYS E:149 , GLU E:348 , EDO E:414 , TYR K:153 , ASP K:343 , LEU K:344
BINDING SITE FOR RESIDUE EDO K 409
16
KC1
SOFTWARE
THR K:309 , ILE K:317 , PRO K:318 , ALA K:319 , ALA K:320
BINDING SITE FOR RESIDUE EDO K 410
17
KC2
SOFTWARE
GLN K:304 , TYR K:305 , HOH K:626
BINDING SITE FOR RESIDUE EDO K 411
18
KC3
SOFTWARE
EDO E:403 , EDO E:414 , CYS K:149 , TYR K:153 , LEU K:344 , VAL K:345 , GLY K:346 , LEU K:347
BINDING SITE FOR RESIDUE EDO K 412
19
KC4
SOFTWARE
GLY G:136 , PRO G:140 , TYR G:170 , GLY K:136 , CYS K:137
BINDING SITE FOR RESIDUE EDO K 413
20
KC5
SOFTWARE
ARG K:241 , ARG K:276 , GLN K:278 , ACT K:415 , HOH K:502 , HOH K:580
BINDING SITE FOR RESIDUE EDO K 414
21
KC6
SOFTWARE
ASP K:277 , GLN K:278 , HIS K:323 , EDO K:414
BINDING SITE FOR RESIDUE ACT K 415
22
KC7
SOFTWARE
LYS K:310 , ALA K:311 , LYS K:349
BINDING SITE FOR RESIDUE ACT K 416
23
KC8
SOFTWARE
PHE K:209 , PRO K:210 , ASN K:211 , GLU K:246 , ARG K:249 , THR K:253
BINDING SITE FOR RESIDUE ACT K 417
24
KC9
SOFTWARE
HOH F:220 , GLU K:162 , ARG K:216 , SER K:239 , DC L:2
BINDING SITE FOR RESIDUE 6AH L 101
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
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 K
Chain L
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 (597 KB)
Header - Asym.Unit
Biol.Unit 1 (105 KB)
Header - Biol.Unit 1
Biol.Unit 2 (105 KB)
Header - Biol.Unit 2
Biol.Unit 3 (105 KB)
Header - Biol.Unit 3
Biol.Unit 4 (102 KB)
Header - Biol.Unit 4
Biol.Unit 5 (103 KB)
Header - Biol.Unit 5
Biol.Unit 6 (103 KB)
Header - Biol.Unit 6
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
4GZ0
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help