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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2IDX
Asym. Unit
Info
Asym.Unit (93 KB)
Biol.Unit 1 (86 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF HUMAN ATP:COBALAMIN ADENOSYLTRANSFERASE BOUND TO ATP.
Authors
:
H. L. Schubert, C. P. Hill
Date
:
15 Sep 06 (Deposition) - 06 Feb 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Atp, Cobalamin, Adenosyltransferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. L. Schubert, C. P. Hill
Structure Of Atp-Bound Human Atp:Cobalamin Adenosyltransferase.
Biochemistry V. 45 15188 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 10)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: CHLORIDE ION (CLa)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
CL
1
Ligand/Ion
CHLORIDE ION
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:108 , THR A:109 , PHE A:110 , TYR A:226
BINDING SITE FOR RESIDUE SO4 A 401
02
AC2
SOFTWARE
HIS C:108 , THR C:109 , PHE C:110 , TYR C:226
BINDING SITE FOR RESIDUE SO4 C 402
03
AC3
SOFTWARE
HIS B:108 , THR B:109 , PHE B:110 , TYR B:226 , HOH B:627
BINDING SITE FOR RESIDUE SO4 B 403
04
AC4
SOFTWARE
ARG A:195 , ARG B:195 , ARG C:195
BINDING SITE FOR RESIDUE CL A 601
05
AC5
SOFTWARE
ASN A:214 , ATP A:607 , HOH A:633 , HOH A:634
BINDING SITE FOR RESIDUE MG A 603
06
AC6
SOFTWARE
ATP B:606 , ASN C:214 , HOH C:652 , HOH C:672
BINDING SITE FOR RESIDUE MG C 604
07
AC7
SOFTWARE
ILE B:58 , ATP B:606 , HOH B:659 , HOH B:669 , HOH B:670 , HOH C:665
BINDING SITE FOR RESIDUE MG B 605
08
AC8
SOFTWARE
ATP A:607 , HOH A:608 , HOH A:631 , HOH A:632 , HOH A:639
BINDING SITE FOR RESIDUE MG A 606
09
AC9
SOFTWARE
ARG A:190 , GLU A:193 , ARG A:194 , ASN A:214 , MG A:603 , MG A:606 , HOH A:608 , HOH A:631 , HOH A:632 , HOH A:633 , HOH A:634 , LYS C:61 , THR C:62 , GLY C:63 , PHE C:67 , SER C:68 , SER C:69 , LYS C:78 , PHE C:83 , HOH C:612 , HOH C:673
BINDING SITE FOR RESIDUE ATP A 607
10
BC1
SOFTWARE
THR B:60 , LYS B:61 , THR B:62 , GLY B:63 , SER B:68 , SER B:69 , LYS B:78 , PHE B:83 , SER B:162 , MG B:605 , HOH B:630 , HOH B:634 , HOH B:659 , HOH B:669 , HOH B:670 , ARG C:190 , GLU C:193 , ARG C:194 , ASN C:214 , MG C:604 , HOH C:652 , HOH C:672
BINDING SITE FOR RESIDUE ATP B 606
[
close Site info
]
SAPs(SNPs)/Variants
(6, 17)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_023471 (I96T, chain A/B/C, )
2: VAR_017204 (A135T, chain B/C, )
3: VAR_017205 (R186W, chain A/B/C, )
4: VAR_017206 (R191W, chain A/B/C, )
5: VAR_017207 (E193K, chain A/B/C, )
6: VAR_017208 (M239K, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_023471
I
96
T
MMAB_HUMAN
Disease (MMAB)
---
A/B/C
I
96
T
2
UniProt
VAR_017204
A
135
T
MMAB_HUMAN
Disease (MMAB)
35648932
B/C
A
135
T
3
UniProt
VAR_017205
R
186
W
MMAB_HUMAN
Polymorphism
28941784
A/B/C
R
186
W
4
UniProt
VAR_017206
R
191
W
MMAB_HUMAN
Disease (MMAB)
---
A/B/C
R
191
W
5
UniProt
VAR_017207
E
193
K
MMAB_HUMAN
Disease (MMAB)
---
A/B/C
E
193
K
6
UniProt
VAR_017208
M
239
K
MMAB_HUMAN
Polymorphism
9593
A/B/C
M
239
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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, 3)
Info
All SCOP Domains
1a: SCOP_d2idxa_ (A:)
1b: SCOP_d2idxb_ (B:)
1c: SCOP_d2idxc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Cobalamin adenosyltransferase-like
(21)
Family
:
automated matches
(17)
Protein domain
:
automated matches
(17)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d2idxa_
A:
1b
d2idxb_
B:
1c
d2idxc_
C:
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_2idxB01 (B:67-240)
1b: CATH_2idxA00 (A:79-240)
1c: CATH_2idxC01 (C:67-240)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Hypothetical Protein Ta1238; Chain: A;
(20)
Homologous Superfamily
:
[code=1.20.1200.10, no name defined]
(20)
Human (Homo sapiens)
(1)
1a
2idxB01
B:67-240
1b
2idxA00
A:79-240
1c
2idxC01
C:67-240
[
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
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 (93 KB)
Header - Asym.Unit
Biol.Unit 1 (86 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
2IDX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help