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.
3C8V
Asym. Unit
Info
Asym.Unit (315 KB)
Biol.Unit 1 (157 KB)
Biol.Unit 2 (154 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 PUTATIVE ACETYLTRANSFERASE (YP_390128.1) FROM DESULFOVIBRIO DESULFURICANS G20 AT 2.28 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
13 Feb 08 (Deposition) - 26 Feb 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.28
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Yp_390128. 1, Putative Acetyltransferase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Acetyltransferase (Yp_390128. 1) From Desulfovibrio Desulfuricans G20 At 2. 28 Resolution
To Be Published
[
close entry info
]
Hetero Components
(4, 81)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
1j: CHLORIDE ION (CLj)
1k: CHLORIDE ION (CLk)
1l: CHLORIDE ION (CLl)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
3a: MAGNESIUM ION (MGa)
4a: SELENOMETHIONINE (MSEa)
4aa: SELENOMETHIONINE (MSEaa)
4ab: SELENOMETHIONINE (MSEab)
4ac: SELENOMETHIONINE (MSEac)
4ad: SELENOMETHIONINE (MSEad)
4ae: SELENOMETHIONINE (MSEae)
4af: SELENOMETHIONINE (MSEaf)
4ag: SELENOMETHIONINE (MSEag)
4ah: SELENOMETHIONINE (MSEah)
4ai: SELENOMETHIONINE (MSEai)
4aj: SELENOMETHIONINE (MSEaj)
4ak: SELENOMETHIONINE (MSEak)
4al: SELENOMETHIONINE (MSEal)
4am: SELENOMETHIONINE (MSEam)
4an: SELENOMETHIONINE (MSEan)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
4q: SELENOMETHIONINE (MSEq)
4r: SELENOMETHIONINE (MSEr)
4s: SELENOMETHIONINE (MSEs)
4t: SELENOMETHIONINE (MSEt)
4u: SELENOMETHIONINE (MSEu)
4v: SELENOMETHIONINE (MSEv)
4w: SELENOMETHIONINE (MSEw)
4x: SELENOMETHIONINE (MSEx)
4y: SELENOMETHIONINE (MSEy)
4z: SELENOMETHIONINE (MSEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
12
Ligand/Ion
CHLORIDE ION
2
EDO
28
Ligand/Ion
1,2-ETHANEDIOL
3
MG
1
Ligand/Ion
MAGNESIUM ION
4
MSE
40
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(36, 36)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:32 , TYR A:39
BINDING SITE FOR RESIDUE CL A 478
02
AC2
SOFTWARE
ARG C:32 , TYR C:39
BINDING SITE FOR RESIDUE CL C 479
03
AC3
SOFTWARE
PHE A:158 , ARG A:176 , TYR A:177
BINDING SITE FOR RESIDUE CL A 479
04
AC4
SOFTWARE
PHE D:158 , ARG D:176 , TYR D:177
BINDING SITE FOR RESIDUE CL D 479
05
AC5
SOFTWARE
PHE B:158 , ARG B:176 , TYR B:177
BINDING SITE FOR RESIDUE CL B 478
06
AC6
SOFTWARE
ASP B:83 , ASN B:301
BINDING SITE FOR RESIDUE CL B 479
07
AC7
SOFTWARE
ARG B:32
BINDING SITE FOR RESIDUE CL B 480
08
AC8
SOFTWARE
GLU C:88 , HIS C:124 , HIS C:150 , HIS C:317
BINDING SITE FOR RESIDUE MG C 480
09
AC9
SOFTWARE
GLN D:182 , SER D:418 , ARG D:422
BINDING SITE FOR RESIDUE EDO D 482
10
BC1
SOFTWARE
GLN B:182 , ILE B:198 , SER B:418 , PHE B:419 , ARG B:422
BINDING SITE FOR RESIDUE EDO B 481
11
BC2
SOFTWARE
LYS A:90 , SER A:127
BINDING SITE FOR RESIDUE EDO A 481
12
BC3
SOFTWARE
GLU A:185 , LYS A:199
BINDING SITE FOR RESIDUE EDO A 482
13
BC4
SOFTWARE
TYR B:180 , GLY B:333 , PHE B:334 , PRO B:356 , PHE B:419 , ARG B:422
BINDING SITE FOR RESIDUE EDO B 482
14
BC5
SOFTWARE
THR B:183 , GLU B:185 , LYS B:199
BINDING SITE FOR RESIDUE EDO B 483
15
BC6
SOFTWARE
GLU D:185 , TRP D:197 , LYS D:199
BINDING SITE FOR RESIDUE EDO D 483
16
BC7
SOFTWARE
ALA A:316 , PHE A:331 , GLY A:333 , PHE A:334 , PRO A:356 , ARG A:422
BINDING SITE FOR RESIDUE EDO A 483
17
BC8
SOFTWARE
GLN A:182 , SER A:418 , PHE A:419 , ARG A:422
BINDING SITE FOR RESIDUE EDO A 484
18
BC9
SOFTWARE
SER D:40 , TYR D:43 , GLN D:458
BINDING SITE FOR RESIDUE EDO D 484
19
CC1
SOFTWARE
GLU A:205 , THR A:407 , ARG A:409
BINDING SITE FOR RESIDUE EDO A 485
20
CC2
SOFTWARE
TRP A:197 , HIS A:207
BINDING SITE FOR RESIDUE EDO A 486
21
CC3
SOFTWARE
ASP D:28 , ARG D:31 , ARG D:32 , SER D:225
BINDING SITE FOR RESIDUE EDO D 485
22
CC4
SOFTWARE
GLU D:205 , HIS D:207 , THR D:407 , ARG D:409
BINDING SITE FOR RESIDUE EDO D 486
23
CC5
SOFTWARE
GLU A:155 , THR A:169 , HIS A:171 , HIS D:171
BINDING SITE FOR RESIDUE EDO A 487
24
CC6
SOFTWARE
HIS B:150 , GLN B:299 , ALA B:316 , HIS B:317 , PHE B:334 , ARG B:422 , ILE B:426
BINDING SITE FOR RESIDUE EDO B 484
25
CC7
SOFTWARE
TYR C:46 , ILE C:454 , ILE C:471 , TYR D:46 , ILE D:454
BINDING SITE FOR RESIDUE EDO C 481
26
CC8
SOFTWARE
TRP B:197 , HIS B:207
BINDING SITE FOR RESIDUE EDO B 485
27
CC9
SOFTWARE
ASP A:83 , LYS A:120 , THR A:121 , LEU A:122 , TYR A:146 , ARG A:284 , ASN A:301
BINDING SITE FOR RESIDUE EDO A 488
28
DC1
SOFTWARE
THR C:183 , GLU C:185 , LYS C:199
BINDING SITE FOR RESIDUE EDO C 482
29
DC2
SOFTWARE
GLU A:342 , GLY D:460 , ARG D:463
BINDING SITE FOR RESIDUE EDO D 487
30
DC3
SOFTWARE
ARG A:10 , HIS D:106
BINDING SITE FOR RESIDUE EDO D 488
31
DC4
SOFTWARE
HIS D:150 , GLN D:299 , ALA D:316 , HIS D:317 , ARG D:422 , ILE D:426
BINDING SITE FOR RESIDUE EDO D 489
32
DC5
SOFTWARE
GLU B:203 , ASP B:398 , GLY B:410 , LYS B:411
BINDING SITE FOR RESIDUE EDO B 486
33
DC6
SOFTWARE
ARG B:31 , ARG B:32
BINDING SITE FOR RESIDUE EDO B 487
34
DC7
SOFTWARE
HIS A:325 , LYS A:347 , ILE A:348
BINDING SITE FOR RESIDUE EDO A 489
35
DC8
SOFTWARE
GLN A:299 , ALA A:316 , HIS A:317 , PHE A:334 , ARG A:422 , ILE A:426
BINDING SITE FOR RESIDUE EDO A 490
36
DC9
SOFTWARE
GLU A:131 , SER A:132 , LYS D:114 , ARG D:139 , ASN D:140
BINDING SITE FOR RESIDUE EDO D 490
[
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
(2, 12)
Info
all CATH domains
1a: CATH_3c8vA04 (A:412-430)
1b: CATH_3c8vB04 (B:412-430)
1c: CATH_3c8vC04 (C:412-430)
1d: CATH_3c8vD04 (D:412-430)
2a: CATH_3c8vC03 (C:229-394)
2b: CATH_3c8vA03 (A:229-394)
2c: CATH_3c8vB03 (B:229-394)
2d: CATH_3c8vD03 (D:229-394)
2e: CATH_3c8vA02 (A:42-228,A:395-411,A:431-475)
2f: CATH_3c8vB02 (B:42-228,B:395-411,B:431-475)
2g: CATH_3c8vC02 (C:42-228,C:395-411,C:431-475)
2h: CATH_3c8vD02 (D:42-228,D:395-411,D:431-475)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
Single helix bin
(16)
Desulfuricans str (Desulfovibrio desulfuricans subsp)
(1)
1a
3c8vA04
A:412-430
1b
3c8vB04
B:412-430
1c
3c8vC04
C:412-430
1d
3c8vD04
D:412-430
Class
:
Mainly Beta
(13760)
Architecture
:
3 Solenoid
(196)
Topology
:
UDP N-Acetylglucosamine Acyltransferase; domain 1
(90)
Homologous Superfamily
:
Hexapeptide repeat proteins
(85)
Desulfuricans str (Desulfovibrio desulfuricans subsp)
(1)
2a
3c8vC03
C:229-394
2b
3c8vA03
A:229-394
2c
3c8vB03
B:229-394
2d
3c8vD03
D:229-394
2e
3c8vA02
A:42-228,A:395-411,A:431-475
2f
3c8vB02
B:42-228,B:395-411,B:431-475
2g
3c8vC02
C:42-228,C:395-411,C:431-475
2h
3c8vD02
D:42-228,D:395-411,D:431-475
[
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
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 (315 KB)
Header - Asym.Unit
Biol.Unit 1 (157 KB)
Header - Biol.Unit 1
Biol.Unit 2 (154 KB)
Header - Biol.Unit 2
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
3C8V
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help