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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2WGH
Asym. Unit
Info
Asym.Unit (221 KB)
Biol.Unit 1 (215 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN RIBONUCLEOTIDE REDUCTASE R1 SUBUNIT (RRM1) IN COMPLEX WITH DATP AND MG.
Authors
:
R. M. Welin, M. Moche, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, A. Johansson, I. Johansson, T. Karlberg, T. Kragh-Nielsen, A. Kotzsch, T. Kotenyova, T. Nyman, C. Persson, J. Sagemark, H. Schueler, P. Schutz, M. I. Siponen, L. Svensson, A. G. Thorsell, L. Tresaugues, S. Van Den Berg, J. Weigelt, M. Wisniewska, P. Nordlund
Date
:
19 Apr 09 (Deposition) - 05 May 09 (Release) - 23 Mar 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Dna Replication, Allosteric Enzyme, Nucleotide-Binding, Cytoplasm, Atp-Binding, Polymorphism, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. W. Fairman, S. R. Wijerathna, M. F. Ahmad, H. Xu, R. Nakano, S. Jha, J. Prendergast, R. M. Welin, S. Flodin, A. Roos, P. Nordlund, Z. Li, T. Walz, C. G. Dealwis
Structural Basis For Allosteric Regulation Of Human Ribonucleotide Reductase By Nucleotide- Induced Oligomerization.
Nat. Struct. Mol. Biol. V. 18 316 2011
[
close entry info
]
Hetero Components
(3, 5)
Info
All Hetero Components
1a: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPa)
1b: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPb)
2a: GLYCEROL (GOLa)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DTP
2
Ligand/Ion
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
2
GOL
1
Ligand/Ion
GLYCEROL
3
MG
2
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:447 , SER A:448 , MET A:602 , THR A:604 , SER A:606 , THR A:607 , HOH A:2019
BINDING SITE FOR RESIDUE GOL A1743
2
AC2
SOFTWARE
DTP A:1745 , HOH A:2114 , HOH A:2115 , HOH A:2118
BINDING SITE FOR RESIDUE MG A1744
3
AC3
SOFTWARE
ASP A:226 , SER A:227 , ILE A:228 , ARG A:256 , ILE A:262 , ALA A:263 , GLY A:264 , MG A:1744 , HOH A:2026 , HOH A:2114 , HOH A:2115 , HOH A:2116 , HOH A:2117 , HOH A:2118 , LYS B:243 , TYR B:285 , VAL B:286 , ASP B:287
BINDING SITE FOR RESIDUE DTP A1745
4
AC4
SOFTWARE
LYS A:243 , TYR A:285 , VAL A:286 , ASP A:287 , ASP B:226 , SER B:227 , ILE B:228 , ARG B:256 , ILE B:262 , ALA B:263 , GLY B:264 , MG B:1746 , HOH B:2109 , HOH B:2110 , HOH B:2111 , HOH B:2112
BINDING SITE FOR RESIDUE DTP B1745
5
AC5
SOFTWARE
DTP B:1745 , HOH B:2110 , HOH B:2111 , HOH B:2112
BINDING SITE FOR RESIDUE MG B1746
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_052052 (K590Q, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_052052
K
590
Q
RIR1_HUMAN
Polymorphism
2228123
A/B
K
590
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: RIBORED_LARGE (A:581-603,B:581-603)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBORED_LARGE
PS00089
Ribonucleotide reductase large subunit signature.
RIR1_HUMAN
581-603
2
A:581-603
B:581-603
[
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
(3, 6)
Info
all PFAM domains
1a: PFAM_Ribonuc_red_lgC_2wghB01 (B:215-739)
1b: PFAM_Ribonuc_red_lgC_2wghB02 (B:215-739)
2a: PFAM_ATP_cone_2wghB03 (B:78-89)
2b: PFAM_ATP_cone_2wghB04 (B:78-89)
3a: PFAM_Ribonuc_red_lgN_2wghB05 (B:141-213)
3b: PFAM_Ribonuc_red_lgN_2wghB06 (B:141-213)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PFL-like
(29)
Family
:
Ribonuc_red_lgC
(23)
Homo sapiens (Human)
(1)
1a
Ribonuc_red_lgC-2wghB01
B:215-739
1b
Ribonuc_red_lgC-2wghB02
B:215-739
Clan
:
no clan defined [family: ATP-cone]
(16)
Family
:
ATP-cone
(16)
Homo sapiens (Human)
(1)
2a
ATP-cone-2wghB03
B:78-89
2b
ATP-cone-2wghB04
B:78-89
Clan
:
no clan defined [family: Ribonuc_red_lgN]
(22)
Family
:
Ribonuc_red_lgN
(22)
Homo sapiens (Human)
(1)
3a
Ribonuc_red_lgN-2wghB05
B:141-213
3b
Ribonuc_red_lgN-2wghB06
B:141-213
[
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
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 (221 KB)
Header - Asym.Unit
Biol.Unit 1 (215 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
2WGH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
