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.
1EF0
Biol. Unit 2
Info
Asym.Unit (145 KB)
Biol.Unit 1 (140 KB)
Biol.Unit 2 (140 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 PI-SCEI MINIPRECURSOR
Authors
:
B. W. Poland, M. -Q. Xu, F. A. Quiocho
Date
:
04 Feb 00 (Deposition) - 07 Jun 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (1x)
Keywords
:
Endonuclease, Protein Splicing, Mini-Precursor, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. W. Poland, M. Q. Xu, F. A. Quiocho
Structural Insights Into The Protein Splicing Mechanism Of Pi-Scei.
J. Biol. Chem. V. 275 16408 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
1a: ZINC ION (ZNa)
1b: ZINC ION (ZNb)
View:
Select:
Label:
Sorry, no Info available
[
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
ILE A:379 , GLU B:80 , HIS B:453 , CYS B:455 , HOH B:719
BINDING SITE FOR RESIDUE ZN B 701
2
AC2
SOFTWARE
GLU A:80 , HIS A:442 , HIS A:453 , CYS A:455 , HOH A:875
BINDING SITE FOR RESIDUE ZN A 701
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: INTEIN_N_TER (A:2-83,B:2-83)
2: INTEIN_ENDONUCLEASE (A:211-359,B:211-359)
3: INTEIN_C_TER (A:430-455,B:430-455)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTEIN_N_TER
PS50817
Intein N-terminal splicing motif profile.
VATA_YEAST
284-366
2
A:2-83
B:2-83
2
INTEIN_ENDONUCLEASE
PS50819
Intein DOD-type homing endonuclease domain profile.
VATA_YEAST
494-642
2
A:211-359
B:211-359
3
INTEIN_C_TER
PS50818
Intein C-terminal splicing motif profile.
VATA_YEAST
713-738
2
A:430-455
B:430-455
[
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, 6)
Info
All SCOP Domains
1a: SCOP_d1ef0a1 (A:1-180,A:416-455)
1b: SCOP_d1ef0b1 (B:1-180,B:416-458)
2a: SCOP_d1ef0a2 (A:181-298)
2b: SCOP_d1ef0a3 (A:299-415)
2c: SCOP_d1ef0b2 (B:181-298)
2d: SCOP_d1ef0b3 (B:299-415)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Hedgehog/intein (Hint) domain
(16)
Superfamily
:
Hedgehog/intein (Hint) domain
(16)
Family
:
Intein (protein splicing domain)
(12)
Protein domain
:
VMA1-derived endonuclease (VDE) PI-Scei intein
(8)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(8)
1a
d1ef0a1
A:1-180,A:416-455
1b
d1ef0b1
B:1-180,B:416-458
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Homing endonuclease-like
(42)
Superfamily
:
Homing endonucleases
(38)
Family
:
Intein endonuclease
(8)
Protein domain
:
VMA1-derived endonuclease (VDE) PI-SceI
(7)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(7)
2a
d1ef0a2
A:181-298
2b
d1ef0a3
A:299-415
2c
d1ef0b2
B:181-298
2d
d1ef0b3
B:299-415
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1ef0A02 (A:183-303)
1b: CATH_1ef0A03 (A:304-398)
2a: CATH_1ef0B01 (B:697-179,B:416-458)
2b: CATH_1ef0A01 (A:699-179,A:416-455)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Endonuclease I-creI
(41)
Homologous Superfamily
:
Homing endonucleases
(40)
Baker's yeast (Saccharomyces cerevisiae)
(8)
1a
1ef0A02
A:183-303
1b
1ef0A03
A:304-398
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Endonuclease - Pi-scei; Chain A, domain 1
(12)
Homologous Superfamily
:
Endonuclease - Pi-scei; Chain A, domain 1
(12)
Baker's yeast (Saccharomyces cerevisiae)
(6)
2a
1ef0B01
B:697-179,B:416-458
2b
1ef0A01
A:699-179,A:416-455
[
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
Asymmetric Unit 2
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 (145 KB)
Header - Asym.Unit
Biol.Unit 1 (140 KB)
Header - Biol.Unit 1
Biol.Unit 2 (140 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
1EF0
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
