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 1
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, 31)
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
5
Ligand/Ion
ACETATE ION
3
EDO
25
Ligand/Ion
1,2-ETHANEDIOL
[
close Hetero Component info
]
Sites
(41, 41)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC2 (SOFTWARE)
20: CC3 (SOFTWARE)
21: CC4 (SOFTWARE)
22: CC5 (SOFTWARE)
23: CC6 (SOFTWARE)
24: CC7 (SOFTWARE)
25: CC8 (SOFTWARE)
26: FC7 (SOFTWARE)
27: FC8 (SOFTWARE)
28: FC9 (SOFTWARE)
29: GC1 (SOFTWARE)
30: HC1 (SOFTWARE)
31: HC9 (SOFTWARE)
32: LC3 (SOFTWARE)
33: LC5 (SOFTWARE)
34: LC6 (SOFTWARE)
35: LC7 (SOFTWARE)
36: MC1 (SOFTWARE)
37: MC7 (SOFTWARE)
38: MC8 (SOFTWARE)
39: MC9 (SOFTWARE)
40: NC7 (SOFTWARE)
41: OC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:333 , GLY A:335 , HIS A:336 , LEU A:337
BINDING SITE FOR RESIDUE EDO A 401
02
AC2
SOFTWARE
ASP A:277 , TRP A:294 , GLN A:304 , TYR A:305 , ARG A:324 , HOH A:605
BINDING SITE FOR RESIDUE EDO A 402
03
AC3
SOFTWARE
TYR A:188 , MET A:214 , HOH A:642 , EDO H:102 , HOH H:201
BINDING SITE FOR RESIDUE EDO A 403
04
AC4
SOFTWARE
EDO A:409 , HOH A:527 , GLU G:348 , LYS G:349
BINDING SITE FOR RESIDUE EDO A 404
05
AC5
SOFTWARE
PHE A:209 , PRO A:210 , ASN A:211 , THR A:212 , GLU A:246 , ARG A:249
BINDING SITE FOR RESIDUE EDO A 405
06
AC6
SOFTWARE
SER A:341 , HOH A:575 , SER G:148
BINDING SITE FOR RESIDUE EDO A 406
07
AC7
SOFTWARE
CYS A:149 , GLU A:348 , ACT A:427 , TYR G:153 , ASP G:343 , LEU G:344
BINDING SITE FOR RESIDUE EDO A 407
08
AC8
SOFTWARE
THR A:179 , LYS A:196 , VAL A:199 , PHE A:201 , HOH A:593
BINDING SITE FOR RESIDUE EDO A 408
09
AC9
SOFTWARE
GLN A:304 , TYR A:305 , ASP A:308 , ALA A:311 , LEU A:344 , TRP A:360 , EDO A:404
BINDING SITE FOR RESIDUE EDO A 409
10
BC1
SOFTWARE
ACT A:423 , HOH A:575
BINDING SITE FOR RESIDUE EDO A 410
11
BC2
SOFTWARE
TYR A:153 , HOH A:501 , CYS G:149 , LEU G:152 , TYR G:153 , GLU G:348
BINDING SITE FOR RESIDUE EDO A 411
12
BC3
SOFTWARE
TRP A:307 , ASP A:308 , THR A:309 , ASN A:312 , ASN A:314 , LEU A:315 , ASP A:358
BINDING SITE FOR RESIDUE EDO A 412
13
BC4
SOFTWARE
ALA A:311 , ASN A:313 , LYS A:349
BINDING SITE FOR RESIDUE EDO A 413
14
BC5
SOFTWARE
LEU A:152 , TYR A:153 , ACT A:423 , HOH A:594 , HOH A:689 , LEU G:152 , TYR G:153 , EDO G:407
BINDING SITE FOR RESIDUE EDO A 414
15
BC6
SOFTWARE
THR A:309 , ILE A:317 , PRO A:318
BINDING SITE FOR RESIDUE EDO A 415
16
BC7
SOFTWARE
ASN A:138 , CYS A:352
BINDING SITE FOR RESIDUE EDO A 416
17
BC8
SOFTWARE
GLY A:227 , ASN A:228 , LEU A:370 , HOH A:666 , ARG E:144
BINDING SITE FOR RESIDUE EDO A 417
18
BC9
SOFTWARE
LEU A:347 , GLU A:348 , LYS A:349 , HOH A:509 , EDO G:405
BINDING SITE FOR RESIDUE EDO A 418
19
CC2
SOFTWARE
GLY A:183 , ASN A:184 , GLN I:204
BINDING SITE FOR RESIDUE EDO A 421
20
CC3
SOFTWARE
LEU A:350 , HOH A:509 , LYS G:301
BINDING SITE FOR RESIDUE EDO A 422
21
CC4
SOFTWARE
SER A:125 , TYR A:153 , PRO A:155 , LEU A:363 , EDO A:410 , EDO A:414 , HOH A:601 , LEU G:152
BINDING SITE FOR RESIDUE ACT A 423
22
CC5
SOFTWARE
HIS A:302 , ASP A:343 , HOH A:528 , ARG G:144 , GLY G:145 , SER G:148 , HOH G:522
BINDING SITE FOR RESIDUE ACT A 424
23
CC6
SOFTWARE
ARG A:144 , GLY A:145 , SER A:148 , GLU A:348 , HOH A:539 , HIS G:302 , ASP G:343
BINDING SITE FOR RESIDUE ACT A 425
24
CC7
SOFTWARE
TYR A:170 , HOH A:650 , GLY E:226 , ASN E:228 , LEU E:370 , HOH E:667
BINDING SITE FOR RESIDUE ACT A 426
25
CC8
SOFTWARE
CYS A:149 , TYR A:153 , LEU A:344 , VAL A:345 , GLY A:346 , LEU A:347 , EDO A:407
BINDING SITE FOR RESIDUE ACT A 427
26
FC7
SOFTWARE
GLU A:162 , SER A:239 , DC D:2 , DG D:4 , DA D:5 , HOH D:201 , DT H:8
BINDING SITE FOR RESIDUE 6AH D 101
27
FC8
SOFTWARE
DA D:6 , DT D:7 , EDO D:103 , THR G:240 , GLU G:242 , HIS G:243
BINDING SITE FOR RESIDUE EDO D 102
28
FC9
SOFTWARE
DT D:7 , EDO D:102 , HOH D:210 , DA H:5 , HOH H:203
BINDING SITE FOR RESIDUE EDO D 103
29
GC1
SOFTWARE
THR A:240 , GLU A:242 , DA D:5
BINDING SITE FOR RESIDUE EDO D 104
30
HC1
SOFTWARE
VAL A:369 , GLY E:133 , LEU E:134 , GLY E:136 , HOH E:549 , HOH E:645
BINDING SITE FOR RESIDUE EDO E 409
31
HC9
SOFTWARE
LYS A:173 , SER E:264 , GLU E:333 , HIS E:336 , HOH E:520 , HOH E:524 , HOH E:571 , HOH E:627
BINDING SITE FOR RESIDUE EDO E 417
32
LC3
SOFTWARE
SER A:148 , ALA A:151 , SER G:341 , EDO G:406 , HOH G:524 , HOH G:594
BINDING SITE FOR RESIDUE EDO G 403
33
LC5
SOFTWARE
EDO A:418 , TYR G:305 , ASP G:308 , ALA G:311 , TRP G:360
BINDING SITE FOR RESIDUE EDO G 405
34
LC6
SOFTWARE
ALA A:151 , EDO G:403 , EDO G:407 , HOH G:524
BINDING SITE FOR RESIDUE EDO G 406
35
LC7
SOFTWARE
LEU A:152 , EDO A:414 , SER G:125 , TYR G:153 , SER G:154 , PRO G:155 , EDO G:406
BINDING SITE FOR RESIDUE EDO G 407
36
MC1
SOFTWARE
ASP A:351 , LEU G:297 , GLY G:298 , PRO G:300
BINDING SITE FOR RESIDUE EDO G 410
37
MC7
SOFTWARE
EDO A:403 , DT H:7 , DT H:8
BINDING SITE FOR RESIDUE EDO H 102
38
MC8
SOFTWARE
MET A:214 , DT H:7 , HOH H:201 , HOH H:202 , HOH H:206
BINDING SITE FOR RESIDUE EDO H 103
39
MC9
SOFTWARE
DC D:9 , DC H:2 , DG H:4
BINDING SITE FOR RESIDUE EDO H 104
40
NC7
SOFTWARE
GLU A:185 , GLU A:186 , CYS I:168 , ILE I:180
BINDING SITE FOR RESIDUE EDO I 407
41
OC4
SOFTWARE
CYS A:168 , LYS A:172 , THR A:182 , ASN A:184 , GLU A:185 , PHE A:189 , GLU I:185
BINDING SITE FOR RESIDUE EDO I 413
[
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 A
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 (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