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.
3CVO
Asym. Unit
Info
Asym.Unit (153 KB)
Biol.Unit 1 (74 KB)
Biol.Unit 2 (72 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 A METHYLTRANSFERASE-LIKE PROTEIN (SPO2022) FROM SILICIBACTER POMEROYI DSS-3 AT 1.80 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
18 Apr 08 (Deposition) - 06 May 08 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Rossmann Fold, 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 Methyltransferase-Like Protein Of Unknown Function (Yp_167254. 1) From Silicibacter Pomeroyi Dss-3 At 1. 80 A Resolution
To Be Published
[
close entry info
]
Hetero Components
(5, 82)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1aa: 1,2-ETHANEDIOL (EDOaa)
1ab: 1,2-ETHANEDIOL (EDOab)
1ac: 1,2-ETHANEDIOL (EDOac)
1ad: 1,2-ETHANEDIOL (EDOad)
1ae: 1,2-ETHANEDIOL (EDOae)
1af: 1,2-ETHANEDIOL (EDOaf)
1ag: 1,2-ETHANEDIOL (EDOag)
1ah: 1,2-ETHANEDIOL (EDOah)
1ai: 1,2-ETHANEDIOL (EDOai)
1aj: 1,2-ETHANEDIOL (EDOaj)
1ak: 1,2-ETHANEDIOL (EDOak)
1al: 1,2-ETHANEDIOL (EDOal)
1am: 1,2-ETHANEDIOL (EDOam)
1an: 1,2-ETHANEDIOL (EDOan)
1ao: 1,2-ETHANEDIOL (EDOao)
1ap: 1,2-ETHANEDIOL (EDOap)
1aq: 1,2-ETHANEDIOL (EDOaq)
1ar: 1,2-ETHANEDIOL (EDOar)
1as: 1,2-ETHANEDIOL (EDOas)
1at: 1,2-ETHANEDIOL (EDOat)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
1o: 1,2-ETHANEDIOL (EDOo)
1p: 1,2-ETHANEDIOL (EDOp)
1q: 1,2-ETHANEDIOL (EDOq)
1r: 1,2-ETHANEDIOL (EDOr)
1s: 1,2-ETHANEDIOL (EDOs)
1t: 1,2-ETHANEDIOL (EDOt)
1u: 1,2-ETHANEDIOL (EDOu)
1v: 1,2-ETHANEDIOL (EDOv)
1w: 1,2-ETHANEDIOL (EDOw)
1x: 1,2-ETHANEDIOL (EDOx)
1y: 1,2-ETHANEDIOL (EDOy)
1z: 1,2-ETHANEDIOL (EDOz)
2a: GLYCEROL (GOLa)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3ae: SELENOMETHIONINE (MSEae)
3af: SELENOMETHIONINE (MSEaf)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
4a: TETRAETHYLENE GLYCOL (PG4a)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
46
Ligand/Ion
1,2-ETHANEDIOL
2
GOL
1
Ligand/Ion
GLYCEROL
3
MSE
32
Mod. Amino Acid
SELENOMETHIONINE
4
PG4
1
Ligand/Ion
TETRAETHYLENE GLYCOL
5
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(50, 50)
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)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:60 , ALA A:61 , ARG A:64
BINDING SITE FOR RESIDUE SO4 A 202
02
AC2
SOFTWARE
ARG B:120 , HIS B:121 , ARG B:158 , TRP B:159
BINDING SITE FOR RESIDUE SO4 B 202
03
AC3
SOFTWARE
ALA D:46 , GLU D:47 , TRP D:69 , ASN D:73 , PRO D:74
BINDING SITE FOR RESIDUE EDO D 202
04
AC4
SOFTWARE
PRO A:90 , SER A:99 , ALA A:101 , GLU D:21 , ARG D:24
BINDING SITE FOR RESIDUE EDO A 203
05
AC5
SOFTWARE
ARG B:10 , PRO B:11 , GLU B:12 , GLY B:40
BINDING SITE FOR RESIDUE EDO B 203
06
AC6
SOFTWARE
ALA A:101 , ARG A:104 , ASP B:100 , PRO D:17 , ALA D:18 , GLU D:21
BINDING SITE FOR RESIDUE EDO A 204
07
AC7
SOFTWARE
HIS B:96 , PRO B:146 , PRO B:201
BINDING SITE FOR RESIDUE EDO B 204
08
AC8
SOFTWARE
THR B:148 , PHE B:179 , GLN B:180
BINDING SITE FOR RESIDUE EDO D 203
09
AC9
SOFTWARE
LYS C:102 , SER C:105
BINDING SITE FOR RESIDUE EDO C 202
10
BC1
SOFTWARE
ARG A:104 , ARG B:196 , THR B:199 , SER B:200
BINDING SITE FOR RESIDUE EDO B 205
11
BC2
SOFTWARE
THR A:54 , PHE A:119 , ARG A:120
BINDING SITE FOR RESIDUE EDO A 205
12
BC3
SOFTWARE
THR D:54 , PHE D:119 , ARG D:120
BINDING SITE FOR RESIDUE EDO D 204
13
BC4
SOFTWARE
ARG A:60 , ARG A:64
BINDING SITE FOR RESIDUE EDO A 206
14
BC5
SOFTWARE
ARG D:10 , PRO D:11 , GLY D:40
BINDING SITE FOR RESIDUE EDO D 205
15
BC6
SOFTWARE
ARG A:120 , HIS A:121
BINDING SITE FOR RESIDUE EDO A 207
16
BC7
SOFTWARE
SER C:99 , ASP C:100
BINDING SITE FOR RESIDUE EDO C 203
17
BC8
SOFTWARE
PRO C:188 , SER D:142 , THR D:144
BINDING SITE FOR RESIDUE EDO D 206
18
BC9
SOFTWARE
THR C:54 , THR C:116 , PHE C:119 , ARG C:120
BINDING SITE FOR RESIDUE EDO C 204
19
CC1
SOFTWARE
HIS B:52 , THR B:54 , ASN B:82 , GLU B:117 , GLY B:118
BINDING SITE FOR RESIDUE EDO B 206
20
CC2
SOFTWARE
LEU D:70 , PRO D:75 , GLU D:80
BINDING SITE FOR RESIDUE EDO D 207
21
CC3
SOFTWARE
GLU D:31 , GLY D:50 , LYS D:51 , HIS D:52 , GLY D:78 , ARG D:120
BINDING SITE FOR RESIDUE EDO D 208
22
CC4
SOFTWARE
ARG A:104
BINDING SITE FOR RESIDUE EDO A 208
23
CC5
SOFTWARE
ARG B:64 , LYS B:67
BINDING SITE FOR RESIDUE EDO B 207
24
CC6
SOFTWARE
ARG B:64
BINDING SITE FOR RESIDUE EDO B 208
25
CC7
SOFTWARE
ARG A:64 , LYS A:67 , TRP A:85
BINDING SITE FOR RESIDUE EDO A 209
26
CC8
SOFTWARE
TRP A:85 , THR A:86 , ASP A:87
BINDING SITE FOR RESIDUE EDO A 210
27
CC9
SOFTWARE
ARG D:60 , ARG D:64
BINDING SITE FOR RESIDUE EDO D 209
28
DC1
SOFTWARE
ARG D:64 , LYS D:67
BINDING SITE FOR RESIDUE EDO D 210
29
DC2
SOFTWARE
ARG C:60 , ARG C:64
BINDING SITE FOR RESIDUE EDO C 205
30
DC3
SOFTWARE
ARG C:60 , ARG C:64 , LYS C:67 , TRP C:85
BINDING SITE FOR RESIDUE EDO C 206
31
DC4
SOFTWARE
ARG A:196 , ARG B:115
BINDING SITE FOR RESIDUE EDO A 211
32
DC5
SOFTWARE
PHE D:166 , LEU D:167 , GLY D:168 , GLN D:180 , GLU D:182 , GLN D:184
BINDING SITE FOR RESIDUE EDO D 211
33
DC6
SOFTWARE
HIS A:52 , THR A:54 , ASN A:82 , GLY A:118
BINDING SITE FOR RESIDUE EDO A 212
34
DC7
SOFTWARE
TRP D:114 , ARG D:115 , THR D:116 , PHE D:119
BINDING SITE FOR RESIDUE EDO D 212
35
DC8
SOFTWARE
TRP B:85 , THR B:86 , ASP B:87
BINDING SITE FOR RESIDUE EDO B 209
36
DC9
SOFTWARE
TRP B:85 , ALA B:112
BINDING SITE FOR RESIDUE EDO B 210
37
EC1
SOFTWARE
SER A:99 , ALA D:20 , GLU D:21
BINDING SITE FOR RESIDUE EDO D 213
38
EC2
SOFTWARE
ARG C:10 , PRO C:11 , LEU C:13
BINDING SITE FOR RESIDUE EDO C 207
39
EC3
SOFTWARE
HIS B:121 , ARG B:145 , ARG B:157 , TRP B:159
BINDING SITE FOR RESIDUE EDO B 211
40
EC4
SOFTWARE
ASP B:59 , GLY B:95
BINDING SITE FOR RESIDUE EDO B 212
41
EC5
SOFTWARE
ASP A:59
BINDING SITE FOR RESIDUE EDO A 213
42
EC6
SOFTWARE
THR B:54 , THR B:116 , PHE B:119 , ARG B:120
BINDING SITE FOR RESIDUE EDO B 213
43
EC7
SOFTWARE
ARG C:60 , ARG C:64
BINDING SITE FOR RESIDUE EDO C 208
44
EC8
SOFTWARE
ALA A:71 , ARG D:60 , ALA D:61 , ARG D:64
BINDING SITE FOR RESIDUE EDO D 214
45
EC9
SOFTWARE
ARG B:60 , ARG B:64
BINDING SITE FOR RESIDUE EDO B 214
46
FC1
SOFTWARE
ARG D:120 , HIS D:121
BINDING SITE FOR RESIDUE EDO D 215
47
FC2
SOFTWARE
ARG A:10 , PRO A:11 , LEU A:13 , ARG A:24 , GLY A:40
BINDING SITE FOR RESIDUE EDO A 214
48
FC3
SOFTWARE
ARG B:115 , ARG B:157 , ARG B:175
BINDING SITE FOR RESIDUE EDO B 215
49
FC4
SOFTWARE
GLU B:29 , ASP B:123 , THR B:148 , GLN B:180
BINDING SITE FOR RESIDUE PG4 D 216
50
FC5
SOFTWARE
SER B:58 , ARG B:60 , TRP B:85 , GLY B:89 , PRO B:90 , THR B:91
BINDING SITE FOR RESIDUE GOL C 209
[
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
(1, 4)
Info
all CATH domains
1a: CATH_3cvoA00 (A:8-201)
1b: CATH_3cvoB00 (B:8-201)
1c: CATH_3cvoC00 (C:8-201)
1d: CATH_3cvoD00 (D:8-201)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Vaccinia Virus protein VP39
(378)
Silicibacter pomeroyi dss-3. Organism_taxid: 246200. Strain: dss-3 / dsm 15171.
(1)
1a
3cvoA00
A:8-201
1b
3cvoB00
B:8-201
1c
3cvoC00
C:8-201
1d
3cvoD00
D:8-201
[
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 (153 KB)
Header - Asym.Unit
Biol.Unit 1 (74 KB)
Header - Biol.Unit 1
Biol.Unit 2 (72 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
3CVO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help