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.
2R6F
Asym. Unit
Info
Asym.Unit (604 KB)
Biol.Unit 1 (593 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 BACILLUS STEAROTHERMOPHILUS UVRA
Authors
:
Y. Inuzuka, D. Pakotiprapha, B. R. Bowman, D. Jeruzalmi, G. L. Verdine
Date
:
05 Sep 07 (Deposition) - 08 Jan 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Uvra, Nucleotide Excision Repair, Dna Repair, Abc Atpase, Atp-Binding Cassette, Dna Damage, Dna Excision, Dna-Binding, Excision Nuclease, Metal-Binding, Nucleotide-Binding, Sos Response, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Pakotiprapha, Y. Inuzuka, B. R. Bowman, G. F. Moolenaar, N. Goosen, D. Jeruzalmi, G. L. Verdine
Crystal Structure Of Bacillus Stearothermophilus Uvra Provides Insight Into Atp-Modulated Dimerization, Uvrb Interaction, And Dna Binding.
Mol. Cell V. 29 122 2008
[
close entry info
]
Hetero Components
(3, 40)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
MSE
30
Mod. Amino Acid
SELENOMETHIONINE
3
ZN
6
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:12 , ASN A:13 , LEU A:32 , GLY A:34 , SER A:35 , GLY A:36 , LYS A:37 , SER A:38 , SER A:39 , TYR A:816 , MSE A:817 , GLN A:821 , HOH A:1007
BINDING SITE FOR RESIDUE ADP A 1000
02
AC2
SOFTWARE
TYR A:475 , ARG A:480 , HIS A:618 , ASN A:619 , VAL A:638 , GLY A:640 , SER A:641 , GLY A:642 , LYS A:643 , SER A:644 , THR A:645 , HOH A:1008
BINDING SITE FOR RESIDUE ADP A 1001
03
AC3
SOFTWARE
CYS A:120 , HIS A:123 , CYS A:250 , CYS A:253
BINDING SITE FOR RESIDUE ZN A 1004
04
AC4
SOFTWARE
CYS A:274 , CYS A:277 , CYS A:404 , CYS A:407
BINDING SITE FOR RESIDUE ZN A 1005
05
AC5
SOFTWARE
CYS A:736 , CYS A:739 , CYS A:759 , CYS A:762
BINDING SITE FOR RESIDUE ZN A 1006
06
AC6
SOFTWARE
HIS B:12 , LEU B:32 , GLY B:34 , SER B:35 , GLY B:36 , LYS B:37 , SER B:38 , SER B:39 , GLY B:563 , TYR B:816 , GLN B:821 , THR B:825
BINDING SITE FOR RESIDUE ADP B 1002
07
AC7
SOFTWARE
TYR B:475 , ARG B:480 , HIS B:618 , ASN B:619 , VAL B:638 , SER B:639 , GLY B:640 , SER B:641 , GLY B:642 , LYS B:643 , SER B:644 , THR B:645 , GLY B:905 , HOH B:1011
BINDING SITE FOR RESIDUE ADP B 1003
08
AC8
SOFTWARE
CYS B:120 , HIS B:123 , CYS B:250 , CYS B:253
BINDING SITE FOR RESIDUE ZN B 1007
09
AC9
SOFTWARE
CYS B:274 , CYS B:277 , CYS B:404 , CYS B:407
BINDING SITE FOR RESIDUE ZN B 1008
10
BC1
SOFTWARE
CYS B:736 , CYS B:739 , CYS B:759 , CYS B:762
BINDING SITE FOR RESIDUE ZN B 1009
[
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
(4, 6)
Info
all CATH domains
1a: CATH_2r6fA03 (A:130-247)
2a: CATH_2r6fA05 (A:587-687,A:827-948)
2b: CATH_2r6fA01 (A:3-90,A:486-586)
3a: CATH_2r6fA04 (A:282-403)
4a: CATH_2r6fA02 (A:91-129,A:248-281,A:404-485)
4b: CATH_2r6fA06 (A:689-826)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
ATP-grasp fold, A domain
(109)
Geobacillus stearothermophilus 10. Organism_taxid: 272567. Strain: 10.
(1)
1a
2r6fA03
A:130-247
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Geobacillus stearothermophilus 10. Organism_taxid: 272567. Strain: 10.
(1)
2a
2r6fA05
A:587-687,A:827-948
2b
2r6fA01
A:3-90,A:486-586
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helicase, Ruva Protein; domain 3
(218)
Homologous Superfamily
:
ABC transporter ATPase domain-like
(1)
Geobacillus stearothermophilus 10. Organism_taxid: 272567. Strain: 10.
(1)
3a
2r6fA04
A:282-403
Architecture
:
Up-down Bundle
(3216)
Topology
:
ABC transporter ATPase like fold
(1)
Homologous Superfamily
:
ABC transporter ATPase like domain
(1)
Geobacillus stearothermophilus 10. Organism_taxid: 272567. Strain: 10.
(1)
4a
2r6fA02
A:91-129,A:248-281,A:404-485
4b
2r6fA06
A:689-826
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_ABC_tran_2r6fB01 (B:644-857)
1b: PFAM_ABC_tran_2r6fB02 (B:644-857)
1c: PFAM_ABC_tran_2r6fB03 (B:644-857)
1d: PFAM_ABC_tran_2r6fB04 (B:644-857)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
ABC_tran
(53)
Geobacillus kaustophilus
(1)
1a
ABC_tran-2r6fB01
B:644-857
1b
ABC_tran-2r6fB02
B:644-857
1c
ABC_tran-2r6fB03
B:644-857
1d
ABC_tran-2r6fB04
B:644-857
[
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 (604 KB)
Header - Asym.Unit
Biol.Unit 1 (593 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
2R6F
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
