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.
3C8V
Biol. Unit 1
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
(2, 37)
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
-1
Ligand/Ion
CHLORIDE ION
2
EDO
17
Ligand/Ion
1,2-ETHANEDIOL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
MSE
20
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(25, 25)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC5 (SOFTWARE)
11: BC7 (SOFTWARE)
12: BC8 (SOFTWARE)
13: CC1 (SOFTWARE)
14: CC2 (SOFTWARE)
15: CC5 (SOFTWARE)
16: CC6 (SOFTWARE)
17: CC8 (SOFTWARE)
18: CC9 (SOFTWARE)
19: DC2 (SOFTWARE)
20: DC3 (SOFTWARE)
21: DC5 (SOFTWARE)
22: DC6 (SOFTWARE)
23: DC7 (SOFTWARE)
24: DC8 (SOFTWARE)
25: 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
AC3
SOFTWARE
PHE A:158 , ARG A:176 , TYR A:177
BINDING SITE FOR RESIDUE CL A 479
03
AC5
SOFTWARE
PHE B:158 , ARG B:176 , TYR B:177
BINDING SITE FOR RESIDUE CL B 478
04
AC6
SOFTWARE
ASP B:83 , ASN B:301
BINDING SITE FOR RESIDUE CL B 479
05
AC7
SOFTWARE
ARG B:32
BINDING SITE FOR RESIDUE CL B 480
06
BC1
SOFTWARE
GLN B:182 , ILE B:198 , SER B:418 , PHE B:419 , ARG B:422
BINDING SITE FOR RESIDUE EDO B 481
07
BC2
SOFTWARE
LYS A:90 , SER A:127
BINDING SITE FOR RESIDUE EDO A 481
08
BC3
SOFTWARE
GLU A:185 , LYS A:199
BINDING SITE FOR RESIDUE EDO A 482
09
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
10
BC5
SOFTWARE
THR B:183 , GLU B:185 , LYS B:199
BINDING SITE FOR RESIDUE EDO B 483
11
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
12
BC8
SOFTWARE
GLN A:182 , SER A:418 , PHE A:419 , ARG A:422
BINDING SITE FOR RESIDUE EDO A 484
13
CC1
SOFTWARE
GLU A:205 , THR A:407 , ARG A:409
BINDING SITE FOR RESIDUE EDO A 485
14
CC2
SOFTWARE
TRP A:197 , HIS A:207
BINDING SITE FOR RESIDUE EDO A 486
15
CC5
SOFTWARE
GLU A:155 , THR A:169 , HIS A:171 , HIS D:171
BINDING SITE FOR RESIDUE EDO A 487
16
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
17
CC8
SOFTWARE
TRP B:197 , HIS B:207
BINDING SITE FOR RESIDUE EDO B 485
18
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
19
DC2
SOFTWARE
GLU A:342 , GLY D:460 , ARG D:463
BINDING SITE FOR RESIDUE EDO D 487
20
DC3
SOFTWARE
ARG A:10 , HIS D:106
BINDING SITE FOR RESIDUE EDO D 488
21
DC5
SOFTWARE
GLU B:203 , ASP B:398 , GLY B:410 , LYS B:411
BINDING SITE FOR RESIDUE EDO B 486
22
DC6
SOFTWARE
ARG B:31 , ARG B:32
BINDING SITE FOR RESIDUE EDO B 487
23
DC7
SOFTWARE
HIS A:325 , LYS A:347 , ILE A:348
BINDING SITE FOR RESIDUE EDO A 489
24
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
25
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 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
(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
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