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.
2E15
Asym. Unit
Info
Asym.Unit (104 KB)
Biol.Unit 1 (99 KB)
Biol.Unit 2 (195 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 ARG173 TO ASN MUTANT OF DIPHTHINE SYNTHASE
Authors
:
H. Mizutani, Y. Matsuura, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
18 Oct 06 (Deposition) - 24 Apr 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (2x)
Keywords
:
Transferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Mizutani, Y. Matsuura, N. Kunishima
Crystal Structure Of Diphthine Synthase From Pyrococcus Horikoshii Ot3
To Be Published
[
close entry info
]
Hetero Components
(4, 13)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
2a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
2b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
3a: S-ADENOSYL-L-HOMOCYSTEINE (SAHa)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
MES
2
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3
SAH
1
Ligand/Ion
S-ADENOSYL-L-HOMOCYSTEINE
4
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG B:46 , HIS B:126 , TYR B:128 , HIS B:243 , HOH B:1591 , HOH B:1657 , HOH B:1681 , HOH B:1789
BINDING SITE FOR RESIDUE SO4 B 1301
02
AC2
SOFTWARE
ARG B:46 , LYS B:129 , LYS B:241 , HIS B:243 , HOH B:1533 , HOH B:1550 , HOH B:1573 , HOH B:1661 , HOH B:1745
BINDING SITE FOR RESIDUE SO4 B 1302
03
AC3
SOFTWARE
ARG A:60 , HOH A:1653
BINDING SITE FOR RESIDUE SO4 A 1303
04
AC4
SOFTWARE
SER A:211 , LEU A:212 , ASN A:213
BINDING SITE FOR RESIDUE SO4 A 1304
05
AC5
SOFTWARE
PRO B:257 , ARG B:258 , HOH B:1773
BINDING SITE FOR RESIDUE SO4 B 1305
06
AC6
SOFTWARE
PRO A:257 , ARG A:258 , HOH A:1563
BINDING SITE FOR RESIDUE SO4 A 1306
07
AC7
SOFTWARE
LEU A:10 , THR A:36 , SER A:37 , GLY A:86 , ASP A:87 , VAL A:90 , SER A:115 , ILE A:116 , PHE A:165 , LEU A:166 , LEU A:206 , ARG A:208 , ALA A:209 , PRO A:233 , HIS A:234 , HOH A:1515 , HOH A:1567 , HOH A:1569
BINDING SITE FOR RESIDUE SAH A 1300
08
AC8
SOFTWARE
PHE A:34 , MET A:39 , THR A:42 , THR A:43 , LEU A:44 , VAL A:57 , HOH A:1715
BINDING SITE FOR RESIDUE MES A 1501
09
AC9
SOFTWARE
ASP B:200 , TYR B:220 , LYS B:222 , GLU B:259
BINDING SITE FOR RESIDUE MES B 1502
10
BC1
SOFTWARE
LEU B:38 , MET B:39 , THR B:42 , THR B:43 , LEU B:44 , HOH B:1639
BINDING SITE FOR RESIDUE GOL B 1401
11
BC2
SOFTWARE
TYR A:128 , HIS A:243 , ASN B:66 , LYS B:132 , GOL B:1404
BINDING SITE FOR RESIDUE GOL A 1402
12
BC3
SOFTWARE
THR A:43 , ARG A:46 , HOH A:1699
BINDING SITE FOR RESIDUE GOL A 1403
13
BC4
SOFTWARE
GOL A:1402 , GLU B:61 , LEU B:65 , THR B:135 , HOH B:1566 , HOH B:1668 , HOH B:1685
BINDING SITE FOR RESIDUE GOL B 1404
[
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2e15a_ (A:)
1b: SCOP_d2e15b_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Tetrapyrrole methylase
(104)
Superfamily
:
Tetrapyrrole methylase
(104)
Family
:
Tetrapyrrole methylase
(96)
Protein domain
:
Diphthine synthase, DphB
(82)
Pyrococcus horikoshii [TaxId: 53953]
(80)
1a
d2e15a_
A:
1b
d2e15b_
B:
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2e15A02 (A:115-265)
1b: CATH_2e15B02 (B:115-265)
2a: CATH_2e15A01 (A:1-114)
2b: CATH_2e15B01 (B:1-114)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
(97)
Homologous Superfamily
:
Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
(97)
Pyrococcus horikoshii ot3. Organism_taxid: 70601. Strain: ot3.
(55)
1a
2e15A02
A:115-265
1b
2e15B02
B:115-265
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Cobalt-precorrin-4 Transmethylase; domain 1
(96)
Homologous Superfamily
:
Cobalt-precorrin-4 Transmethylase; Domain 1
(96)
Pyrococcus horikoshii ot3. Organism_taxid: 70601. Strain: ot3.
(55)
2a
2e15A01
A:1-114
2b
2e15B01
B:1-114
[
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 (104 KB)
Header - Asym.Unit
Biol.Unit 1 (99 KB)
Header - Biol.Unit 1
Biol.Unit 2 (195 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
2E15
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
