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.
1P8O
Asym. Unit
Info
Asym.Unit (153 KB)
Biol.Unit 1 (148 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURAL AND FUNCTIONAL IMPORTANCE OF FIRST-SHELL METAL LIGANDS IN THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE I.
Authors
:
E. Cama, F. A. Emig, D. E. Ash, D. W. Christianson
Date
:
07 May 03 (Deposition) - 17 Jun 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.96
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Hydrolase, Urea Cycle, Arginine Metabolism, Binuclear Manganese Cluster
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Cama, F. A. Emig, D. E. Ash, D. W. Christianson
Structural And Functional Importance Of First-Shell Metal Ligands In The Binuclear Manganese Cluster Of Arginase I
Biochemistry V. 42 7748 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 6)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
1c: MANGANESE (II) ION (MNc)
1d: MANGANESE (II) ION (MNd)
1e: MANGANESE (II) ION (MNe)
1f: MANGANESE (II) ION (MNf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MN
6
Ligand/Ion
MANGANESE (II) ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:124 , HIS A:126 , ASP A:232 , ASP A:234 , MN A:501 , HOH A:817
BINDING SITE FOR RESIDUE MN A 500
2
AC2
SOFTWARE
HIS A:101 , ASP A:124 , ASP A:232 , MN A:500
BINDING SITE FOR RESIDUE MN A 501
3
AC3
SOFTWARE
ASP B:124 , HIS B:126 , ASP B:232 , ASP B:234 , MN B:503 , HOH B:800
BINDING SITE FOR RESIDUE MN B 502
4
AC4
SOFTWARE
HIS B:101 , ASP B:124 , ASP B:232 , MN B:502
BINDING SITE FOR RESIDUE MN B 503
5
AC5
SOFTWARE
ASP C:124 , HIS C:126 , ASP C:232 , ASP C:234 , MN C:505 , HOH C:816
BINDING SITE FOR RESIDUE MN C 504
6
AC6
SOFTWARE
HIS C:101 , ASP C:124 , ASP C:232 , MN C:504
BINDING SITE FOR RESIDUE MN C 505
[
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, 3)
Info
All PROSITE Patterns/Profiles
1: ARGINASE_1 (A:230-251,B:230-251,C:230-251)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ARGINASE_1
PS01053
Arginase family signature.
ARGI1_RAT
230-251
3
A:230-251
B:230-251
C:230-251
[
close PROSITE info
]
Exons
(8, 24)
Info
All Exons
Exon 1.1 (A:6-19 | B:6-19 | C:6-19)
Exon 1.2 (A:20-44 | B:20-44 | C:20-44)
Exon 1.3 (A:44-102 | B:44-102 | C:44-102)
Exon 1.4 (A:102-155 | B:102-155 | C:102-155)
Exon 1.5 (A:156-187 | B:156-187 | C:156-187)
Exon 1.6 (A:187-222 | B:187-222 | C:187-222)
Exon 1.7 (A:222-268 | B:222-268 | C:222-268)
Exon 1.8 (A:268-319 | B:268-319 | C:268-319)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/1.6
7: Boundary 1.6/1.7
8: Boundary 1.7/1.8
9: Boundary 1.8/-
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
1.1
ENSRNOT00000017911
1
ENSRNOE00000127362
chr1:
20998894-20999025
132
ARGI1_RAT
1-19
19
3
A:6-19
B:6-19
C:6-19
14
14
14
1.2
ENSRNOT00000017911
2
ENSRNOE00000127505
chr1:
21003810-21003882
73
ARGI1_RAT
20-44
25
3
A:20-44
B:20-44
C:20-44
25
25
25
1.3
ENSRNOT00000017911
3
ENSRNOE00000127596
chr1:
21005814-21005988
175
ARGI1_RAT
44-102
59
3
A:44-102
B:44-102
C:44-102
59
59
59
1.4
ENSRNOT00000017911
4
ENSRNOE00000126918
chr1:
21008032-21008191
160
ARGI1_RAT
102-155
54
3
A:102-155
B:102-155
C:102-155
54
54
54
1.5
ENSRNOT00000017911
5
ENSRNOE00000126971
chr1:
21009513-21009607
95
ARGI1_RAT
156-187
32
3
A:156-187
B:156-187
C:156-187
32
32
32
1.6
ENSRNOT00000017911
6
ENSRNOE00000127033
chr1:
21010045-21010149
105
ARGI1_RAT
187-222
36
3
A:187-222
B:187-222
C:187-222
36
36
36
1.7
ENSRNOT00000017911
7
ENSRNOE00000127086
chr1:
21010337-21010473
137
ARGI1_RAT
222-268
47
3
A:222-268
B:222-268
C:222-268
47
47
47
1.8
ENSRNOT00000017911
8
ENSRNOE00000127695
chr1:
21010716-21011266
551
ARGI1_RAT
268-323
56
3
A:268-319
B:268-319
C:268-319
52
52
52
[
close EXON info
]
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d1p8oa_ (A:)
1b: SCOP_d1p8ob_ (B:)
1c: SCOP_d1p8oc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Arginase/deacetylase
(138)
Superfamily
:
Arginase/deacetylase
(138)
Family
:
Arginase-like amidino hydrolases
(97)
Protein domain
:
Arginase
(73)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(34)
1a
d1p8oa_
A:
1b
d1p8ob_
B:
1c
d1p8oc_
C:
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1p8oA00 (A:6-319)
1b: CATH_1p8oB00 (B:6-319)
1c: CATH_1p8oC00 (C:6-319)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Arginase; Chain A
(84)
Homologous Superfamily
:
[code=3.40.800.10, no name defined]
(63)
Norway rat (Rattus norvegicus)
(31)
1a
1p8oA00
A:6-319
1b
1p8oB00
B:6-319
1c
1p8oC00
C:6-319
[
close CATH info
]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_Arginase_1p8oC01 (C:6-305)
1b: PFAM_Arginase_1p8oC02 (C:6-305)
1c: PFAM_Arginase_1p8oC03 (C:6-305)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Arginase
(56)
Family
:
Arginase
(37)
Rattus norvegicus (Rat)
(19)
1a
Arginase-1p8oC01
C:6-305
1b
Arginase-1p8oC02
C:6-305
1c
Arginase-1p8oC03
C:6-305
[
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 (153 KB)
Header - Asym.Unit
Biol.Unit 1 (148 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
1P8O
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help