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.
3EP6
Asym. Unit
Info
Asym.Unit (58 KB)
Biol.Unit 1 (54 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN ADOMETDC D174N MUTANT COMPLEXED WITH S-ADENOSYLMETHIONINE METHYL ESTER AND NO PUTRESCINE BOUND
Authors
:
S. Bale, M. M. Lopez, G. I. Makhatadze, Q. Fang, A. E. Pegg, S. E. Ealick
Date
:
29 Sep 08 (Deposition) - 23 Dec 08 (Release) - 23 Dec 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Adometdc With Mutation In Putrescine Binding Site, Decarboxylase, Lyase, Pyruvate, S-Adenosyl-L-Methionine, Spermidine Biosynthesis, Zymogen
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Bale, M. M. Lopez, G. I. Makhatadze, Q. Fang, A. E. Pegg, S. E. Ealick
Structural Basis For Putrescine Activation Of Human S-Adenosylmethionine Decarboxylase.
Biochemistry V. 47 13404 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: PYRUVIC ACID (PYRa)
2a: S-ADENOSYLMETHIONINE METHYL ESTER (SMMa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PYR
1
Ligand/Ion
PYRUVIC ACID
2
SMM
1
Ligand/Ion
S-ADENOSYLMETHIONINE METHYL ESTER
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:69 , LYS A:80 , THR A:81 , HIS A:243 , SMM A:368 , VAL B:64 , LEU B:65
BINDING SITE FOR RESIDUE PYR A 68
2
AC2
SOFTWARE
PYR A:68 , SER A:69 , THR A:81 , CYS A:82 , PHE A:223 , ASN A:224 , CYS A:226 , GLY A:227 , TYR A:228 , SER A:229 , ILE A:244 , THR A:245 , PRO A:246 , GLU A:247 , PHE B:7 , LEU B:65 , SER B:66 , GLU B:67
BINDING SITE FOR RESIDUE SMM A 368
[
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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: ADOMETDC (B:62-67)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADOMETDC
PS01336
S-adenosylmethionine decarboxylase signature.
DCAM_HUMAN
62-72
1
B:62-67
[
close PROSITE info
]
Exons
(9, 10)
Info
All Exons
Exon 1.1a (- | B:4-37 (gaps))
Exon 1.3 (- | B:37-66)
Exon 1.4 (A:69-108 | B:66-67)
Exon 1.5 (A:109-143 | -)
Exon 1.6 (A:143-157 | -)
Exon 1.7 (A:157-205 (gaps) | -)
Exon 1.8 (A:206-236 | -)
Exon 1.9c (A:237-288 | -)
Exon 1.10b (A:299-327 | -)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9c
09: Boundary 1.9c/1.10b
10: Boundary 1.10b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000368885
1a
ENSE00002153832
chr6:
111195973-111196418
446
DCAM_HUMAN
1-37
37
1
-
B:4-37 (gaps)
-
34
1.3
ENST00000368885
3
ENSE00002172835
chr6:
111208708-111208794
87
DCAM_HUMAN
37-66
30
1
-
B:37-66
-
30
1.4
ENST00000368885
4
ENSE00002150406
chr6:
111210060-111210186
127
DCAM_HUMAN
66-108
43
2
A:69-108
B:66-67
40
2
1.5
ENST00000368885
5
ENSE00002165815
chr6:
111211457-111211559
103
DCAM_HUMAN
109-143
35
1
A:109-143
-
35
-
1.6
ENST00000368885
6
ENSE00002194062
chr6:
111213364-111213406
43
DCAM_HUMAN
143-157
15
1
A:143-157
-
15
-
1.7
ENST00000368885
7
ENSE00002152985
chr6:
111213502-111213646
145
DCAM_HUMAN
157-205
49
1
A:157-205 (gaps)
-
49
-
1.8
ENST00000368885
8
ENSE00002167612
chr6:
111213938-111214030
93
DCAM_HUMAN
206-236
31
1
A:206-236
-
31
-
1.9c
ENST00000368885
9c
ENSE00000839942
chr6:
111214113-111214268
156
DCAM_HUMAN
237-288
52
1
A:237-288
-
52
-
1.10b
ENST00000368885
10b
ENSE00002196756
chr6:
111214679-111216916
2238
DCAM_HUMAN
289-334
46
1
A:299-327
-
29
-
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3ep6A00 (A:69-327)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
4-Layer Sandwich
(459)
Topology
:
S-adenosylmethionine decarboxylase
(29)
Homologous Superfamily
:
S-adenosylmethionine decarboxylase
(29)
Human (Homo sapiens)
(25)
1a
3ep6A00
A:69-327
[
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 (58 KB)
Header - Asym.Unit
Biol.Unit 1 (54 KB)
Header - Biol.Unit 1
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
3EP6
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
