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.
PLEASE WAIT...
Getting 'Exon' information from database.
3Q9E
Asym. Unit
Info
Asym.Unit (649 KB)
Biol.Unit 1 (115 KB)
Biol.Unit 2 (116 KB)
Biol.Unit 3 (115 KB)
Biol.Unit 4 (115 KB)
Biol.Unit 5 (116 KB)
Biol.Unit 6 (115 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF H159A APAH COMPLEXED WITH ACETYLSPERMINE
Authors
:
P. M. Lombardi, D. W. Christianson
Date
:
07 Jan 11 (Deposition) - 02 Mar 11 (Release) - 30 Mar 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,I (1x)
Biol. Unit 2: B,F (1x)
Biol. Unit 3: C,K (1x)
Biol. Unit 4: D,J (1x)
Biol. Unit 5: E,H (1x)
Biol. Unit 6: G,L (1x)
Keywords
:
Hdac, Polyamine, Arginase Fold, Deacetylase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. M. Lombardi, H. D. Angell, D. A. Whittington, E. F. Flynn, K. R. Rajashankar, D. W. Christianson
Structure Of Prokaryotic Polyamine Deacetylase Reveals Evolutionary Functional Relationships With Eukaryotic Histone Deacetylases .
Biochemistry V. 50 1808 2011
[
close entry info
]
Hetero Components
(4, 48)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
1e: POTASSIUM ION (Ke)
1f: POTASSIUM ION (Kf)
1g: POTASSIUM ION (Kg)
1h: POTASSIUM ION (Kh)
1i: POTASSIUM ION (Ki)
1j: POTASSIUM ION (Kj)
1k: POTASSIUM ION (Kk)
1l: POTASSIUM ION (Kl)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
2d: SODIUM ION (NAd)
2e: SODIUM ION (NAe)
2f: SODIUM ION (NAf)
2g: SODIUM ION (NAg)
2h: SODIUM ION (NAh)
2i: SODIUM ION (NAi)
2j: SODIUM ION (NAj)
2k: SODIUM ION (NAk)
2l: SODIUM ION (NAl)
3a: N-[3-({4-[(3-AMINOPROPYL)AMINO]BUT... (SP5a)
3b: N-[3-({4-[(3-AMINOPROPYL)AMINO]BUT... (SP5b)
3c: N-[3-({4-[(3-AMINOPROPYL)AMINO]BUT... (SP5c)
3d: N-[3-({4-[(3-AMINOPROPYL)AMINO]BUT... (SP5d)
3e: N-[3-({4-[(3-AMINOPROPYL)AMINO]BUT... (SP5e)
3f: N-[3-({4-[(3-AMINOPROPYL)AMINO]BUT... (SP5f)
3g: N-[3-({4-[(3-AMINOPROPYL)AMINO]BUT... (SP5g)
3h: N-[3-({4-[(3-AMINOPROPYL)AMINO]BUT... (SP5h)
3i: N-[3-({4-[(3-AMINOPROPYL)AMINO]BUT... (SP5i)
3j: N-[3-({4-[(3-AMINOPROPYL)AMINO]BUT... (SP5j)
3k: N-[3-({4-[(3-AMINOPROPYL)AMINO]BUT... (SP5k)
3l: N-[3-({4-[(3-AMINOPROPYL)AMINO]BUT... (SP5l)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
4f: ZINC ION (ZNf)
4g: ZINC ION (ZNg)
4h: ZINC ION (ZNh)
4i: ZINC ION (ZNi)
4j: ZINC ION (ZNj)
4k: ZINC ION (ZNk)
4l: ZINC ION (ZNl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
12
Ligand/Ion
POTASSIUM ION
2
NA
12
Ligand/Ion
SODIUM ION
3
SP5
12
Ligand/Ion
N-[3-({4-[(3-AMINOPROPYL)AMINO]BUTYL}AMINO)PROPYL]ACETAMIDE
4
ZN
12
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(48, 48)
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: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:117 , PRO A:156 , HIS A:158 , GLY A:167 , TYR A:168 , HIS A:197 , PHE A:225 , TYR A:323 , ZN A:344 , TYR I:83 , GLU I:106
BINDING SITE FOR RESIDUE SP5 A 401
02
AC2
SOFTWARE
ASP A:193 , ASP A:195 , HIS A:197 , SER A:216 , LEU A:217
BINDING SITE FOR RESIDUE K A 342
03
AC3
SOFTWARE
PHE A:206 , ARG A:209 , VAL A:212 , THR A:243 , HOH A:345
BINDING SITE FOR RESIDUE NA A 343
04
AC4
SOFTWARE
ASP A:195 , HIS A:197 , ASP A:284 , SP5 A:401
BINDING SITE FOR RESIDUE ZN A 344
05
AC5
SOFTWARE
TYR B:19 , GLU B:117 , HIS B:158 , GLY B:167 , TYR B:168 , HIS B:197 , TYR B:323 , ZN B:344 , HOH B:499 , TYR F:83 , GLU F:106
BINDING SITE FOR RESIDUE SP5 B 402
06
AC6
SOFTWARE
ASP B:193 , ASP B:195 , HIS B:197 , SER B:216 , LEU B:217
BINDING SITE FOR RESIDUE K B 342
07
AC7
SOFTWARE
PHE B:206 , ARG B:209 , VAL B:212 , THR B:243 , HOH B:345
BINDING SITE FOR RESIDUE NA B 343
08
AC8
SOFTWARE
ASP B:195 , HIS B:197 , ASP B:284 , SP5 B:402
BINDING SITE FOR RESIDUE ZN B 344
09
AC9
SOFTWARE
GLU C:117 , HIS C:158 , GLY C:167 , TYR C:168 , ASP C:284 , TYR C:323 , ZN C:344 , TYR K:83 , GLU K:106
BINDING SITE FOR RESIDUE SP5 C 403
10
BC1
SOFTWARE
ASP C:193 , ASP C:195 , HIS C:197 , SER C:216 , LEU C:217
BINDING SITE FOR RESIDUE K C 342
11
BC2
SOFTWARE
PHE C:206 , ARG C:209 , VAL C:212 , THR C:243 , HOH C:345
BINDING SITE FOR RESIDUE NA C 343
12
BC3
SOFTWARE
ASP C:195 , HIS C:197 , ASP C:284 , TYR C:323 , SP5 C:403
BINDING SITE FOR RESIDUE ZN C 344
13
BC4
SOFTWARE
TYR D:19 , GLU D:117 , PRO D:156 , HIS D:158 , GLY D:167 , TYR D:168 , HIS D:197 , PHE D:225 , ILE D:291 , TYR D:323 , ZN D:344 , HOH D:769 , TYR J:83 , GLU J:106
BINDING SITE FOR RESIDUE SP5 D 404
14
BC5
SOFTWARE
ASP D:193 , ASP D:195 , HIS D:197 , SER D:216 , LEU D:217
BINDING SITE FOR RESIDUE K D 342
15
BC6
SOFTWARE
PHE D:206 , ARG D:209 , VAL D:212 , THR D:243 , HOH D:345
BINDING SITE FOR RESIDUE NA D 343
16
BC7
SOFTWARE
ASP D:195 , HIS D:197 , ASP D:284 , TYR D:323 , SP5 D:404
BINDING SITE FOR RESIDUE ZN D 344
17
BC8
SOFTWARE
GLU E:117 , PRO E:156 , HIS E:158 , GLY E:167 , TYR E:168 , CYS E:169 , TYR E:323 , ZN E:344 , TYR H:83 , GLU H:106
BINDING SITE FOR RESIDUE SP5 E 405
18
BC9
SOFTWARE
ASP E:193 , ASP E:195 , HIS E:197 , SER E:216 , LEU E:217
BINDING SITE FOR RESIDUE K E 342
19
CC1
SOFTWARE
PHE E:206 , ARG E:209 , VAL E:212 , THR E:243 , HOH E:345
BINDING SITE FOR RESIDUE NA E 343
20
CC2
SOFTWARE
ASP E:195 , HIS E:197 , ASP E:284 , SP5 E:405
BINDING SITE FOR RESIDUE ZN E 344
21
CC3
SOFTWARE
TYR B:83 , GLU B:106 , TYR F:19 , GLU F:117 , PRO F:156 , HIS F:158 , GLY F:167 , TYR F:168 , CYS F:169 , ASP F:195 , HIS F:197 , PHE F:225 , TYR F:323 , ZN F:344
BINDING SITE FOR RESIDUE SP5 F 406
22
CC4
SOFTWARE
ASP F:193 , ASP F:195 , HIS F:197 , SER F:216 , LEU F:217 , HIS F:218
BINDING SITE FOR RESIDUE K F 342
23
CC5
SOFTWARE
PHE F:206 , ARG F:209 , VAL F:212 , THR F:243 , HOH F:904
BINDING SITE FOR RESIDUE NA F 343
24
CC6
SOFTWARE
ASP F:195 , HIS F:197 , ASP F:284 , TYR F:323 , SP5 F:406
BINDING SITE FOR RESIDUE ZN F 344
25
CC7
SOFTWARE
GLU G:117 , HIS G:158 , GLY G:167 , TYR G:168 , HIS G:197 , TYR G:323 , ZN G:344 , HOH G:897 , GLU L:106
BINDING SITE FOR RESIDUE SP5 G 407
26
CC8
SOFTWARE
ASP G:193 , ASP G:195 , HIS G:197 , SER G:216 , LEU G:217 , HIS G:218
BINDING SITE FOR RESIDUE K G 342
27
CC9
SOFTWARE
PHE G:206 , ARG G:209 , VAL G:212 , THR G:243 , HOH G:345
BINDING SITE FOR RESIDUE NA G 343
28
DC1
SOFTWARE
ASP G:195 , HIS G:197 , ASP G:284 , SP5 G:407
BINDING SITE FOR RESIDUE ZN G 344
29
DC2
SOFTWARE
GLU E:106 , TYR H:19 , GLU H:117 , PRO H:156 , HIS H:158 , GLY H:167 , TYR H:168 , CYS H:169 , HIS H:197 , PRO H:290 , TYR H:323 , ZN H:344
BINDING SITE FOR RESIDUE SP5 H 408
30
DC3
SOFTWARE
ASP H:193 , ASP H:195 , HIS H:197 , SER H:216 , LEU H:217
BINDING SITE FOR RESIDUE K H 342
31
DC4
SOFTWARE
PHE H:206 , ARG H:209 , VAL H:212 , THR H:243 , HOH H:906
BINDING SITE FOR RESIDUE NA H 343
32
DC5
SOFTWARE
ASP H:195 , HIS H:197 , ASP H:284 , GLY H:321 , SP5 H:408
BINDING SITE FOR RESIDUE ZN H 344
33
DC6
SOFTWARE
GLU A:106 , TYR I:19 , GLU I:117 , PRO I:156 , HIS I:158 , GLY I:167 , TYR I:168 , CYS I:169 , PHE I:225 , PRO I:290 , TYR I:323 , ZN I:344
BINDING SITE FOR RESIDUE SP5 I 409
34
DC7
SOFTWARE
ASP I:193 , ASP I:195 , HIS I:197 , SER I:216 , LEU I:217
BINDING SITE FOR RESIDUE K I 342
35
DC8
SOFTWARE
PHE I:206 , ARG I:209 , VAL I:212 , THR I:243 , HOH I:345
BINDING SITE FOR RESIDUE NA I 343
36
DC9
SOFTWARE
ASP I:195 , HIS I:197 , ASP I:284 , GLY I:321 , SP5 I:409
BINDING SITE FOR RESIDUE ZN I 344
37
EC1
SOFTWARE
TYR D:83 , GLU D:106 , TYR J:19 , GLU J:117 , HIS J:158 , GLY J:167 , TYR J:168 , CYS J:169 , TYR J:323 , ZN J:344
BINDING SITE FOR RESIDUE SP5 J 410
38
EC2
SOFTWARE
ASP J:193 , ASP J:195 , HIS J:197 , SER J:216 , LEU J:217
BINDING SITE FOR RESIDUE K J 342
39
EC3
SOFTWARE
PHE J:206 , ARG J:209 , VAL J:212 , THR J:243 , HOH J:345
BINDING SITE FOR RESIDUE NA J 343
40
EC4
SOFTWARE
ASP J:195 , HIS J:197 , ASP J:284 , SP5 J:410
BINDING SITE FOR RESIDUE ZN J 344
41
EC5
SOFTWARE
TYR C:83 , TYR K:19 , GLU K:117 , PRO K:156 , HIS K:158 , GLY K:167 , TYR K:168 , CYS K:169 , TYR K:323 , ZN K:344 , HOH K:804
BINDING SITE FOR RESIDUE SP5 K 411
42
EC6
SOFTWARE
ASP K:193 , ASP K:195 , HIS K:197 , SER K:216 , LEU K:217
BINDING SITE FOR RESIDUE K K 342
43
EC7
SOFTWARE
PHE K:206 , ARG K:209 , VAL K:212 , THR K:243 , HOH K:345
BINDING SITE FOR RESIDUE NA K 343
44
EC8
SOFTWARE
ASP K:195 , HIS K:197 , ASP K:284 , GLY K:321 , SP5 K:411
BINDING SITE FOR RESIDUE ZN K 344
45
EC9
SOFTWARE
TYR G:83 , GLU G:106 , TYR L:19 , GLU L:117 , PRO L:156 , HIS L:158 , GLY L:167 , TYR L:168 , CYS L:169 , HIS L:197 , ILE L:291 , TYR L:323 , ZN L:344
BINDING SITE FOR RESIDUE SP5 L 412
46
FC1
SOFTWARE
ASP L:193 , ASP L:195 , HIS L:197 , SER L:216 , LEU L:217
BINDING SITE FOR RESIDUE K L 342
47
FC2
SOFTWARE
PHE L:206 , ARG L:209 , VAL L:212 , THR L:243
BINDING SITE FOR RESIDUE NA L 343
48
FC3
SOFTWARE
ASP L:195 , HIS L:197 , ASP L:284 , SP5 L:412
BINDING SITE FOR RESIDUE ZN L 344
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 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.
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 B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
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 (649 KB)
Header - Asym.Unit
Biol.Unit 1 (115 KB)
Header - Biol.Unit 1
Biol.Unit 2 (116 KB)
Header - Biol.Unit 2
Biol.Unit 3 (115 KB)
Header - Biol.Unit 3
Biol.Unit 4 (115 KB)
Header - Biol.Unit 4
Biol.Unit 5 (116 KB)
Header - Biol.Unit 5
Biol.Unit 6 (115 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
3Q9E
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
