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.
2B3Y
Biol. Unit 2
Info
Asym.Unit (310 KB)
Biol.Unit 1 (152 KB)
Biol.Unit 2 (152 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 A MONOCLINIC CRYSTAL FORM OF HUMAN CYTOSOLIC ACONITASE (IRP1)
Authors
:
J. Dupuy, J. C. Fontecilla-Camps, A. Volbeda
Date
:
22 Sep 05 (Deposition) - 10 Jan 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Irp1 Ire-Irp1 Aconitase Activity, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Dupuy, A. Volbeda, P. Carpentier, C. Darnault, J. M. Moulis, J. C. Fontecilla-Camps
Crystal Structure Of Human Iron Regulatory Protein 1 As Cytosolic Aconitase
Structure V. 14 129 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 4)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
2a: FORMIC ACID (FMTa)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
4a: IRON/SULFUR CLUSTER (SF4a)
4b: IRON/SULFUR CLUSTER (SF4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
FMT
1
Ligand/Ion
FORMIC ACID
3
GOL
-1
Ligand/Ion
GLYCEROL
4
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
HIS B:126 , ASP B:205 , ILE B:507 , ARG B:536 , ARG B:541 , ACT B:891 , SF4 B:1000 , FMT B:1001 , HOH B:1186
BINDING SITE FOR RESIDUE ACT B 890
2
AC3
SOFTWARE
GLN B:86 , PHE B:88 , THR B:89 , ARG B:713 , SER B:778 , ARG B:780 , ACT B:890 , FMT B:1001
BINDING SITE FOR RESIDUE ACT B 891
3
AC5
SOFTWARE
ILE B:176 , ILE B:177 , HIS B:178 , HIS B:207 , SER B:436 , CYS B:437 , CYS B:503 , CYS B:506 , ASN B:535 , ACT B:890 , HOH B:1186
BINDING SITE FOR RESIDUE SF4 B 1000
4
AC8
SOFTWARE
ASP B:205 , SER B:206 , ARG B:536 , SER B:778 , SER B:779 , ACT B:890 , ACT B:891
BINDING SITE FOR RESIDUE FMT B 1001
[
close Site info
]
SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_069413 (T318M, chain B, )
2: VAR_048180 (A395D, chain B, )
3: VAR_048181 (G486R, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_069413
T
318
M
ACOC_HUMAN
Polymorphism
---
B
T
318
M
2
UniProt
VAR_048180
A
395
D
ACOC_HUMAN
Polymorphism
3814519
B
A
395
D
3
UniProt
VAR_048181
G
486
R
ACOC_HUMAN
Polymorphism
34630459
B
G
486
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: ACONITASE_1 (B:429-445)
2: ACONITASE_2 (B:495-508)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ACONITASE_1
PS00450
Aconitase family signature 1.
ACOC_HUMAN
429-445
1
-
B:429-445
2
ACONITASE_2
PS01244
Aconitase family signature 2.
ACOC_HUMAN
495-508
1
-
B:495-508
[
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2b3ya2 (A:2-630)
1b: SCOP_d2b3yb2 (B:2-630)
2a: SCOP_d2b3ya1 (A:631-889)
2b: SCOP_d2b3yb1 (B:631-889)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Aconitase iron-sulfur domain
(20)
Superfamily
:
Aconitase iron-sulfur domain
(20)
Family
:
Aconitase iron-sulfur domain
(20)
Protein domain
:
Iron-responsive element binding protein 1, N-terminal domain
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2b3ya2
A:2-630
1b
d2b3yb2
B:2-630
Fold
:
The swivelling beta/beta/alpha domain
(136)
Superfamily
:
LeuD/IlvD-like
(25)
Family
:
LeuD-like
(19)
Protein domain
:
ron-responsive element binding protein 1, C-terminal domain
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d2b3ya1
A:631-889
2b
d2b3yb1
B:631-889
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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 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 (310 KB)
Header - Asym.Unit
Biol.Unit 1 (152 KB)
Header - Biol.Unit 1
Biol.Unit 2 (152 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
2B3Y
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help