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.
4O1P
Asym. Unit
Info
Asym.Unit (474 KB)
Biol.Unit 1 (236 KB)
Biol.Unit 2 (235 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 RNASE L IN COMPLEX WITH 2-5A AND AMP-PNP
Authors
:
H. Huang, E. Zeqiraj, D. F. Ceccarelli, F. Sicheri
Date
:
16 Dec 13 (Deposition) - 05 Feb 14 (Release) - 24 Dec 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Ankyrin Repeat-Kinase-Rnase, Rna Cleavage, 2-5A, Transferase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Huang, E. Zeqiraj, B. Dong, B. K. Jha, N. M. Duffy, S. Orlicky, N. Thevakumaran, M. Talukdar, M. C. Pillon, D. F. Ceccarelli, L. C. Wan Y. C. Juang, D. Y. Mao, C. Gaughan, M. A. Brinton, A. A. Perelygin, I. Kourinov, A. Guarne, R. H. Silverman, F. Sicheri
Dimeric Structure Of Pseudokinase Rnase L Bound To 2-5A Reveals A Basis For Interferon-Induced Antiviral Activity.
Mol. Cell V. 53 221 2014
[
close entry info
]
Hetero Components
(3, 16)
Info
All Hetero Components
1a: [[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-... (25La)
1b: [[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-... (25Lb)
1c: [[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-... (25Lc)
1d: [[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-... (25Ld)
2a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
2b: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPb)
2c: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPc)
2d: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
25L
4
Ligand/Ion
[[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-[[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-3-HYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-3-HYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE
2
ANP
4
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3
MG
8
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(16, 16)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:370 , THR A:372 , ALA A:373 , ILE A:377 , ALA A:388 , LYS A:390 , ALA A:433 , CYS A:435 , THR A:438 , GLN A:486 , ASN A:487 , LEU A:489 , ASP A:500 , ASP A:502 , MG A:902 , MG A:903 , HOH A:1046 , HOH A:1084
BINDING SITE FOR RESIDUE ANP A 901
02
AC2
SOFTWARE
ASP A:500 , ASP A:502 , ANP A:901 , MG A:903
BINDING SITE FOR RESIDUE MG A 902
03
AC3
SOFTWARE
ASN A:487 , ASP A:500 , ANP A:901 , MG A:902 , HOH A:1046
BINDING SITE FOR RESIDUE MG A 903
04
AC4
SOFTWARE
TRP A:56 , TRP A:58 , SER A:63 , GLN A:66 , LYS A:87 , ASN A:89 , ILE A:99 , ASN A:122 , PHE A:124 , GLU A:129 , TYR A:133 , ARG A:153 , LYS A:164 , HOH A:1002 , HOH A:1020 , HOH A:1024 , HOH A:1028 , HOH A:1035 , HOH A:1052 , HOH A:1064 , HOH A:1112 , HOH A:1222 , ARG B:307 , ARG B:308 , TYR B:310 , ARG B:353 , PHE B:362 , HOH B:1089
BINDING SITE FOR RESIDUE 25L A 904
05
AC5
SOFTWARE
ALA B:370 , THR B:372 , ALA B:373 , ILE B:377 , ALA B:388 , LYS B:390 , ALA B:433 , CYS B:435 , THR B:438 , GLN B:486 , ASN B:487 , LEU B:489 , ASP B:500 , ASP B:502 , MG B:902 , MG B:903 , HOH B:1023 , HOH B:1076
BINDING SITE FOR RESIDUE ANP B 901
06
AC6
SOFTWARE
ARG B:398 , ASP B:500 , ASP B:502 , ANP B:901 , MG B:903
BINDING SITE FOR RESIDUE MG B 902
07
AC7
SOFTWARE
ASN B:487 , ASP B:500 , ANP B:901 , MG B:902
BINDING SITE FOR RESIDUE MG B 903
08
AC8
SOFTWARE
ARG A:307 , ARG A:308 , TYR A:310 , ARG A:353 , PHE A:362 , HOH A:1071 , HOH A:1110 , TRP B:56 , TRP B:58 , SER B:63 , GLN B:66 , LYS B:87 , ASN B:89 , ILE B:99 , ASP B:120 , ASN B:122 , PHE B:124 , GLU B:129 , TYR B:133 , ARG B:153 , LYS B:164 , HOH B:1003 , HOH B:1012 , HOH B:1102 , HOH B:1122 , HOH B:1140 , HOH B:1165 , HOH B:1233
BINDING SITE FOR RESIDUE 25L B 904
09
AC9
SOFTWARE
ALA C:370 , THR C:372 , ALA C:373 , ILE C:377 , ALA C:388 , LYS C:390 , ALA C:433 , CYS C:435 , THR C:438 , GLN C:486 , ASN C:487 , LEU C:489 , ASP C:500 , ASP C:502 , MG C:902 , MG C:903 , HOH C:1011 , HOH C:1023 , HOH C:1056 , HOH C:1072 , HOH C:1194
BINDING SITE FOR RESIDUE ANP C 901
10
BC1
SOFTWARE
ASP C:500 , ASP C:502 , ANP C:901 , MG C:903 , HOH C:1011
BINDING SITE FOR RESIDUE MG C 902
11
BC2
SOFTWARE
ASN C:487 , ASP C:500 , ANP C:901 , MG C:902
BINDING SITE FOR RESIDUE MG C 903
12
BC3
SOFTWARE
TRP C:56 , TRP C:58 , SER C:63 , GLN C:66 , LYS C:87 , ASN C:89 , ASP C:120 , ASN C:122 , PHE C:124 , GLU C:129 , TYR C:133 , ARG C:153 , LYS C:164 , HOH C:1003 , HOH C:1005 , HOH C:1007 , HOH C:1021 , HOH C:1048 , HOH C:1052 , HOH C:1059 , HOH C:1087 , HOH C:1100 , HOH C:1108 , HOH C:1148 , HOH C:1208 , HOH C:1216 , ARG D:307 , ARG D:308 , TYR D:310 , ARG D:353 , PHE D:362 , SER D:426 , HOH D:1012
BINDING SITE FOR RESIDUE 25L C 904
13
BC4
SOFTWARE
ALA D:370 , THR D:372 , ALA D:373 , ILE D:377 , ALA D:388 , LYS D:390 , ARG D:398 , ALA D:433 , CYS D:435 , THR D:438 , GLN D:486 , ASN D:487 , LEU D:489 , ASP D:500 , ASP D:502 , MG D:902 , MG D:903 , HOH D:1132
BINDING SITE FOR RESIDUE ANP D 901
14
BC5
SOFTWARE
GLN D:486 , ASN D:487 , ASP D:500 , ANP D:901 , MG D:903
BINDING SITE FOR RESIDUE MG D 902
15
BC6
SOFTWARE
ASP D:482 , ASN D:487 , ASP D:500 , ANP D:901 , MG D:902
BINDING SITE FOR RESIDUE MG D 903
16
BC7
SOFTWARE
ARG C:307 , TYR C:310 , ARG C:353 , PHE C:362 , HOH C:1130 , TRP D:56 , TRP D:58 , SER D:63 , GLN D:66 , LYS D:87 , ASN D:89 , ASN D:122 , PHE D:124 , GLU D:129 , TYR D:133 , ARG D:153 , LYS D:164 , HOH D:1003 , HOH D:1041 , HOH D:1055 , HOH D:1155 , HOH D:1156 , HOH D:1189 , HOH D:1205 , HOH D:1232
BINDING SITE FOR RESIDUE 25L D 904
[
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
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 (474 KB)
Header - Asym.Unit
Biol.Unit 1 (236 KB)
Header - Biol.Unit 1
Biol.Unit 2 (235 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
4O1P
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
