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.
4QFX
Asym. Unit
Info
Asym.Unit (355 KB)
Biol.Unit 1 (346 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 THE TETRAMERIC DGTP/DATP-BOUND SAMHD1 (RN206) MUTANT CATALYTIC CORE
Authors
:
L. M. I. Koharudin, Y. Wu, M. Delucia, J. Mehrens, A. M. Gronenborn, J. Ah
Date
:
21 May 14 (Deposition) - 15 Oct 14 (Release) - 03 Dec 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Deoxynucleoside Triphosphate Triphosphohydrolase, 2'-Deoxynucleotide- 5'-Triphosphate, Hiv Restriction Factor, Dntpase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. M. Koharudin, Y. Wu, M. Delucia, J. Mehrens, A. M. Gronenborn, J. Ahn
Structural Basis Of Allosteric Activation Of Sterile Alpha Motif And Histidine-Aspartate Domain-Containing Protein 1 (Samhd1) By Nucleoside Triphosphates.
J. Biol. Chem. V. 289 32617 2014
[
close entry info
]
Hetero Components
(3, 20)
Info
All Hetero Components
1a: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTa)
1b: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTb)
1c: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTc)
1d: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTd)
1e: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTe)
1f: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTf)
1g: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTg)
1h: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTh)
2a: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPa)
2b: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPb)
2c: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPc)
2d: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPd)
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
DGT
8
Ligand/Ion
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2
DTP
4
Ligand/Ion
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
3
MG
8
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(20, 20)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:155 , VAL A:156 , ARG A:451 , LYS A:455 , HOH A:877 , LYS C:523 , DTP C:701 , MG C:704 , LYS D:116 , ILE D:118 , ASP D:137 , GLN D:142 , ARG D:145 , PHE D:165 , HOH D:855
BINDING SITE FOR RESIDUE DGT A 701
02
AC2
SOFTWARE
GLN A:149 , LEU A:150 , ARG A:164 , ARG A:206 , HIS A:210 , HIS A:215 , HIS A:233 , LYS A:312 , TYR A:315 , ASP A:319 , ARG A:366 , TYR A:374 , GLN A:375 , MG A:707 , HOH A:805 , HOH A:838 , HOH A:847 , HOH A:858 , HOH A:869 , HOH A:870 , HOH A:873
BINDING SITE FOR RESIDUE DGT A 702
03
AC3
SOFTWARE
ARG A:333 , ARG A:352 , LYS A:354 , ASN A:358 , LYS A:523 , MG A:705 , HOH A:829 , VAL B:117 , ILE B:118 , ASN B:119 , VAL C:156 , PHE C:157 , ARG C:372 , HIS C:376 , VAL C:378 , DGT C:702
BINDING SITE FOR RESIDUE DTP A 703
04
AC4
SOFTWARE
LYS A:116 , VAL A:117 , ILE A:118 , ASP A:137 , GLN A:142 , ARG A:145 , PHE A:165 , MG A:706 , HOH A:813 , HOH A:862 , HOH A:865 , LYS B:523 , DTP B:703 , TYR D:155 , VAL D:156 , VAL D:378 , ARG D:451 , LYS D:455 , HOH D:859 , HOH D:877
BINDING SITE FOR RESIDUE DGT A 704
05
AC5
SOFTWARE
DTP A:703 , DGT C:702
BINDING SITE FOR RESIDUE MG A 705
06
AC6
SOFTWARE
LYS A:116 , DGT A:704 , DTP B:703
BINDING SITE FOR RESIDUE MG A 706
07
AC7
SOFTWARE
ARG A:206 , ASP A:309 , ASP A:311 , DGT A:702 , HOH A:869 , HOH A:873
BINDING SITE FOR RESIDUE MG A 707
08
AC8
SOFTWARE
TYR B:155 , VAL B:156 , VAL B:378 , ARG B:451 , LYS B:455 , HOH B:822 , HOH B:825 , HOH B:842 , HOH B:844 , HOH B:884 , LYS C:116 , VAL C:117 , ASP C:137 , GLN C:142 , ARG C:145 , PHE C:165 , MG C:705 , LYS D:523 , DTP D:701
BINDING SITE FOR RESIDUE DGT B 701
09
AC9
SOFTWARE
GLN B:149 , LEU B:150 , ARG B:164 , ARG B:206 , HIS B:210 , HIS B:215 , HIS B:233 , LYS B:312 , TYR B:315 , ASP B:319 , ARG B:366 , TYR B:374 , GLN B:375 , MG B:704 , HOH B:808 , HOH B:818 , HOH B:820 , HOH B:829 , HOH B:845 , HOH B:862 , HOH B:905 , HOH B:906
BINDING SITE FOR RESIDUE DGT B 702
10
BC1
SOFTWARE
VAL A:117 , ILE A:118 , ASN A:119 , DGT A:704 , MG A:706 , ARG B:333 , PHE B:337 , ARG B:352 , LYS B:354 , ASN B:358 , LYS B:523 , HOH B:815 , HOH B:824 , HOH B:885 , HOH B:887 , VAL D:156 , PHE D:157 , ARG D:372 , HIS D:376 , LYS D:377
BINDING SITE FOR RESIDUE DTP B 703
11
BC2
SOFTWARE
DGT B:702 , HOH B:878 , HOH B:905
BINDING SITE FOR RESIDUE MG B 704
12
BC3
SOFTWARE
VAL A:156 , PHE A:157 , ILE A:325 , ARG A:372 , HIS A:376 , LYS A:377 , VAL A:378 , DGT A:701 , ARG C:333 , PHE C:337 , ARG C:352 , LYS C:354 , ASN C:358 , LYS C:523 , MG C:704 , HOH C:803 , VAL D:117 , ASN D:119
BINDING SITE FOR RESIDUE DTP C 701
13
BC4
SOFTWARE
LYS A:523 , DTP A:703 , MG A:705 , LYS B:116 , VAL B:117 , ASP B:137 , GLN B:142 , ARG B:145 , PHE B:165 , TYR C:155 , VAL C:156 , VAL C:378 , ARG C:451 , LYS C:455 , HOH C:810 , HOH C:812 , HOH C:832 , HOH C:835 , HOH C:862
BINDING SITE FOR RESIDUE DGT C 702
14
BC5
SOFTWARE
GLN C:149 , LEU C:150 , ARG C:164 , ARG C:206 , HIS C:210 , HIS C:215 , HIS C:233 , LYS C:312 , TYR C:315 , ASP C:319 , ARG C:366 , TYR C:374 , GLN C:375 , MG C:706 , HOH C:809 , HOH C:819 , HOH C:855 , HOH C:857 , HOH C:860 , HOH C:866
BINDING SITE FOR RESIDUE DGT C 703
15
BC6
SOFTWARE
DGT A:701 , DTP C:701 , LYS D:116
BINDING SITE FOR RESIDUE MG C 704
16
BC7
SOFTWARE
DGT B:701 , HOH B:842 , LYS C:116 , DTP D:701
BINDING SITE FOR RESIDUE MG C 705
17
BC8
SOFTWARE
LYS C:312 , DGT C:703 , HOH C:857 , HOH C:860
BINDING SITE FOR RESIDUE MG C 706
18
BC9
SOFTWARE
VAL B:156 , PHE B:157 , ILE B:325 , ARG B:372 , HIS B:376 , LYS B:377 , DGT B:701 , HOH B:884 , VAL C:117 , ASN C:119 , MG C:705 , ARG D:333 , PHE D:337 , ARG D:352 , LYS D:354 , ASN D:358 , LYS D:523 , HOH D:817 , HOH D:843 , HOH D:844
BINDING SITE FOR RESIDUE DTP D 701
19
CC1
SOFTWARE
GLN D:149 , LEU D:150 , ARG D:164 , ARG D:206 , HIS D:210 , HIS D:215 , HIS D:233 , LYS D:312 , TYR D:315 , ASP D:319 , ARG D:366 , HIS D:370 , TYR D:374 , GLN D:375 , MG D:703 , HOH D:803 , HOH D:832 , HOH D:838 , HOH D:884
BINDING SITE FOR RESIDUE DGT D 702
20
CC2
SOFTWARE
LYS D:312 , DGT D:702 , HOH D:890
BINDING SITE FOR RESIDUE MG D 703
[
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 (355 KB)
Header - Asym.Unit
Biol.Unit 1 (346 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
4QFX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
