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.
4PEG
Asym. Unit
Info
Asym.Unit (321 KB)
Biol.Unit 1 (68 KB)
Biol.Unit 2 (69 KB)
Biol.Unit 3 (68 KB)
Biol.Unit 4 (67 KB)
Biol.Unit 5 (67 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
DBR1 IN COMPLEX WITH GUANOSINE-5'-MONOPHOSPHATE
Authors
:
E. J. Montemayor, A. Katolik, N. E. Clark, A. B. Taylor, J. P. Schuermann D. J. Combs, R. Johnsson, S. P. Holloway, S. W. Stevens, M. J. Damha, P. J
Date
:
23 Apr 14 (Deposition) - 27 Aug 14 (Release) - 01 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Keywords
:
Nuclease, Phosphodiesterase, Metallohydrolase, Metallophosphoesterase, Lariat Rna, Hydrolase, Metalloenzyme
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. J. Montemayor, A. Katolik, N. E. Clark, A. B. Taylor, J. P. Schuermann, D. J. Combs, R. Johnsson, S. P. Holloway, S. W. Stevens, M. J. Damha, P. J. Hart
Structural Basis Of Lariat Rna Recognition By The Intron Debranching Enzyme Dbr1.
Nucleic Acids Res. V. 42 10845 2014
[
close entry info
]
Hetero Components
(4, 17)
Info
All Hetero Components
1a: GUANOSINE-5'-MONOPHOSPHATE (5GPa)
1b: GUANOSINE-5'-MONOPHOSPHATE (5GPb)
1c: GUANOSINE-5'-MONOPHOSPHATE (5GPc)
1d: GUANOSINE-5'-MONOPHOSPHATE (5GPd)
1e: GUANOSINE-5'-MONOPHOSPHATE (5GPe)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: MANGANESE (II) ION (MNa)
3b: MANGANESE (II) ION (MNb)
3c: MANGANESE (II) ION (MNc)
3d: MANGANESE (II) ION (MNd)
3e: MANGANESE (II) ION (MNe)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
5GP
5
Ligand/Ion
GUANOSINE-5'-MONOPHOSPHATE
2
GOL
2
Ligand/Ion
GLYCEROL
3
MN
5
Ligand/Ion
MANGANESE (II) ION
4
SO4
5
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(17, 17)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:45 , ASN A:90 , HIS A:180 , HIS A:230 , 5GP A:402 , HOH A:629
binding site for residue MN A 401
02
AC2
SOFTWARE
ASP A:45 , ASN A:90 , HIS A:91 , GLY A:201 , ASP A:205 , HIS A:230 , MET A:231 , HIS A:232 , MN A:401 , HOH A:607 , HOH A:629 , HOH A:633 , HOH A:653 , HOH A:717
binding site for residue 5GP A 402
03
AC3
SOFTWARE
ARG A:50 , ASN A:95 , HIS A:99 , PRO A:146 , HOH A:507
binding site for residue SO4 A 403
04
AC4
SOFTWARE
SER A:38 , LEU A:83 , ASN A:122 , LYS A:266 , THR A:267 , HOH A:680
binding site for residue GOL A 404
05
AC5
SOFTWARE
ASP B:45 , ASN B:90 , HIS B:180 , HIS B:230 , 5GP B:402 , HOH B:626
binding site for residue MN B 401
06
AC6
SOFTWARE
ASP B:45 , ASN B:90 , HIS B:91 , GLY B:201 , ASP B:205 , LEU B:209 , HIS B:230 , MET B:231 , HIS B:232 , MN B:401 , HOH B:534 , HOH B:626 , HOH B:689
binding site for residue 5GP B 402
07
AC7
SOFTWARE
ARG B:50 , ASN B:95 , HIS B:99 , HOH B:532 , HOH B:642 , HOH B:644
binding site for residue SO4 B 403
08
AC8
SOFTWARE
SER B:38 , ASN B:122 , LYS B:266 , THR B:267
binding site for residue GOL B 404
09
AC9
SOFTWARE
ASP C:45 , ASN C:90 , HIS C:180 , HIS C:230 , 5GP C:402 , HOH C:663
binding site for residue MN C 401
10
AD1
SOFTWARE
ASP C:45 , ASN C:90 , HIS C:91 , GLY C:201 , ASP C:205 , HIS C:230 , MET C:231 , HIS C:232 , MN C:401 , HOH C:602 , HOH C:663
binding site for residue 5GP C 402
11
AD2
SOFTWARE
ARG C:50 , ASN C:95 , HIS C:99 , PRO C:146 , HOH C:503 , HOH C:505 , HOH C:645 , HOH C:646
binding site for residue SO4 C 403
12
AD3
SOFTWARE
ASP D:45 , ASN D:90 , HIS D:180 , HIS D:230 , 5GP D:402 , HOH D:712
binding site for residue MN D 401
13
AD4
SOFTWARE
ASP D:45 , ASN D:90 , HIS D:91 , GLY D:201 , ASP D:205 , HIS D:230 , MET D:231 , HIS D:232 , MN D:401 , HOH D:693 , HOH D:712
binding site for residue 5GP D 402
14
AD5
SOFTWARE
ARG D:50 , ASN D:95 , HIS D:99 , PRO D:146 , HOH D:506 , HOH D:570 , HOH D:588
binding site for residue SO4 D 403
15
AD6
SOFTWARE
ASP E:45 , ASN E:90 , HIS E:180 , HIS E:230 , 5GP E:402 , HOH E:677
binding site for residue MN E 401
16
AD7
SOFTWARE
ASP E:45 , ASN E:90 , HIS E:91 , GLY E:201 , ASP E:205 , HIS E:230 , MET E:231 , HIS E:232 , MN E:401 , HOH E:586 , HOH E:623 , HOH E:636 , HOH E:677
binding site for residue 5GP E 402
17
AD8
SOFTWARE
ARG E:50 , ASN E:95 , HIS E:99 , HOH E:591 , HOH E:602 , HOH E:644
binding site for residue SO4 E 403
[
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
(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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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 A
Chain B
Chain C
Chain D
Chain E
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 (321 KB)
Header - Asym.Unit
Biol.Unit 1 (68 KB)
Header - Biol.Unit 1
Biol.Unit 2 (69 KB)
Header - Biol.Unit 2
Biol.Unit 3 (68 KB)
Header - Biol.Unit 3
Biol.Unit 4 (67 KB)
Header - Biol.Unit 4
Biol.Unit 5 (67 KB)
Header - Biol.Unit 5
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
4PEG
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
