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.
1XXH
Biol. Unit 1
Info
Asym.Unit (574 KB)
Biol.Unit 1 (288 KB)
Biol.Unit 2 (285 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ATPGS BOUND E. COLI CLAMP LOADER COMPLEX
Authors
:
S. L. Kazmirski, M. Podobnik, T. F. Weitze, M. O'Donnell, J. Kuriyan
Date
:
05 Nov 04 (Deposition) - 07 Dec 04 (Release) - 15 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.45
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: F,G,H,I,J (1x)
Keywords
:
Aaa+ Atpase Clamp Loader, Gamma Complex, Dna Polymerase Iii, Dna Replication, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. L. Kazmirski, M. Podobnik, T. F. Weitze, M. O'Donnell, J. Kuriyan
Structural Analysis Of The Inactive State Of The Escherichi Coli Dna Polymerase Clamp-Loader Complex
Proc. Natl. Acad. Sci. Usa V. 101 16750 2004
[
close entry info
]
Hetero Components
(3, 14)
Info
All Hetero Components
1a: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSa)
1b: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSb)
1c: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSc)
1d: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSd)
2a: SELENOMETHIONINE (MSEa)
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)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
4f: ZINC ION (ZNf)
4g: ZINC ION (ZNg)
4h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AGS
2
Ligand/Ion
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
2
MSE
11
Mod. Amino Acid
SELENOMETHIONINE
3
PO4
1
Ligand/Ion
PHOSPHATE ION
4
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC2 (SOFTWARE)
7: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS C:64 , CYS C:73 , CYS C:76 , CYS C:79
BINDING SITE FOR RESIDUE ZN C 401
2
AC2
SOFTWARE
CYS D:64 , CYS D:73 , GLY D:74 , CYS D:76 , CYS D:79
BINDING SITE FOR RESIDUE ZN D 402
3
AC3
SOFTWARE
CYS B:64 , CYS B:73 , GLY B:74 , CYS B:76 , CYS B:79
BINDING SITE FOR RESIDUE ZN B 403
4
AC4
SOFTWARE
CYS E:50 , SER E:58 , CYS E:59 , GLY E:60 , CYS E:62 , CYS E:65
BINDING SITE FOR RESIDUE ZN E 404
5
AC9
SOFTWARE
THR C:46 , ARG C:47 , GLY C:48 , VAL C:49 , LYS C:51 , THR C:52 , ARG C:215
BINDING SITE FOR RESIDUE PO4 C 1300
6
BC2
SOFTWARE
ALA D:7 , ARG D:11 , PRO D:12 , VAL D:19 , ARG D:47 , GLY D:48 , VAL D:49 , GLY D:50 , LYS D:51 , THR D:52 , SER D:53 , THR D:157 , LEU D:214 , ARG D:215 , LEU D:218
BINDING SITE FOR RESIDUE AGS D 801
7
BC3
SOFTWARE
ALA B:7 , ARG B:11 , VAL B:19 , THR B:46 , ARG B:47 , GLY B:48 , VAL B:49 , GLY B:50 , LYS B:51 , THR B:52 , SER B:53 , THR B:157 , LEU B:214 , ARG B:215
BINDING SITE FOR RESIDUE AGS B 802
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(6, 20)
Info
All SCOP Domains
1a: SCOP_d1xxhe1 (E:208-334)
1b: SCOP_d1xxhj1 (J:208-334)
2a: SCOP_d1xxha1 (A:212-338)
2b: SCOP_d1xxhf1 (F:212-338)
3a: SCOP_d1xxhb1 (B:243-368)
3b: SCOP_d1xxhc1 (C:243-368)
3c: SCOP_d1xxhd1 (D:243-368)
3d: SCOP_d1xxhg1 (G:243-368)
3e: SCOP_d1xxhh1 (H:243-368)
3f: SCOP_d1xxhi1 (I:243-368)
4a: SCOP_d1xxhe2 (E:1-207)
4b: SCOP_d1xxhj2 (J:1-207)
5a: SCOP_d1xxha2 (A:1-211)
5b: SCOP_d1xxhf2 (F:1-211)
6a: SCOP_d1xxhb2 (B:5-242)
6b: SCOP_d1xxhc2 (C:5-242)
6c: SCOP_d1xxhd2 (D:5-242)
6d: SCOP_d1xxhg2 (G:5-242)
6e: SCOP_d1xxhh2 (H:5-242)
6f: SCOP_d1xxhi2 (I:5-242)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
post-AAA+ oligomerization domain-like
(22)
Superfamily
:
post-AAA+ oligomerization domain-like
(22)
Family
:
DNA polymerase III clamp loader subunits, C-terminal domain
(18)
Protein domain
:
delta prime subunit
(4)
Escherichia coli [TaxId: 562]
(4)
1a
d1xxhe1
E:208-334
1b
d1xxhj1
J:208-334
Protein domain
:
delta subunit
(4)
Escherichia coli [TaxId: 562]
(4)
2a
d1xxha1
A:212-338
2b
d1xxhf1
F:212-338
Protein domain
:
gamma subunit
(4)
Escherichia coli [TaxId: 562]
(3)
3a
d1xxhb1
B:243-368
3b
d1xxhc1
C:243-368
3c
d1xxhd1
D:243-368
3d
d1xxhg1
G:243-368
3e
d1xxhh1
H:243-368
3f
d1xxhi1
I:243-368
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
Extended AAA-ATPase domain
(92)
Protein domain
:
delta prime subunit of DNA polymerase III, N-domain
(6)
Escherichia coli [TaxId: 562]
(6)
4a
d1xxhe2
E:1-207
4b
d1xxhj2
J:1-207
Protein domain
:
delta subunit of DNA polymerase III, N-domain
(5)
Escherichia coli [TaxId: 562]
(5)
5a
d1xxha2
A:1-211
5b
d1xxhf2
F:1-211
Protein domain
:
gamma subunit of DNA polymerase III, N-domain
(4)
Escherichia coli [TaxId: 562]
(3)
6a
d1xxhb2
B:5-242
6b
d1xxhc2
C:5-242
6c
d1xxhd2
D:5-242
6d
d1xxhg2
G:5-242
6e
d1xxhh2
H:5-242
6f
d1xxhi2
I:5-242
[
close SCOP info
]
CATH Domains
(5, 30)
Info
all CATH domains
1a: CATH_1xxhC01 (C:3-178)
1b: CATH_1xxhA01 (A:2-142)
1c: CATH_1xxhF01 (F:2-142)
1d: CATH_1xxhH01 (H:3-178)
1e: CATH_1xxhB01 (B:5-178)
1f: CATH_1xxhD01 (D:5-178)
1g: CATH_1xxhG01 (G:5-178)
1h: CATH_1xxhI01 (I:5-178)
1i: CATH_1xxhE01 (E:2-167)
1j: CATH_1xxhJ01 (J:2-167)
2a: CATH_1xxhB02 (B:179-241)
2b: CATH_1xxhD02 (D:179-241)
2c: CATH_1xxhG02 (G:179-241)
2d: CATH_1xxhH02 (H:179-241)
2e: CATH_1xxhI02 (I:179-241)
2f: CATH_1xxhA02 (A:143-213)
2g: CATH_1xxhF02 (F:143-213)
2h: CATH_1xxhC02 (C:179-241)
3a: CATH_1xxhE02 (E:168-207)
3b: CATH_1xxhJ02 (J:168-207)
4a: CATH_1xxhE03 (E:208-334)
4b: CATH_1xxhJ03 (J:208-334)
4c: CATH_1xxhB03 (B:242-363)
4d: CATH_1xxhG03 (G:242-363)
4e: CATH_1xxhC03 (C:242-368)
4f: CATH_1xxhD03 (D:242-368)
4g: CATH_1xxhH03 (H:242-368)
4h: CATH_1xxhI03 (I:242-368)
5a: CATH_1xxhA03 (A:214-338)
5b: CATH_1xxhF03 (F:214-338)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Escherichia coli. Organism_taxid: 562.
(54)
1a
1xxhC01
C:3-178
1b
1xxhA01
A:2-142
1c
1xxhF01
F:2-142
1d
1xxhH01
H:3-178
1e
1xxhB01
B:5-178
1f
1xxhD01
D:5-178
1g
1xxhG01
G:5-178
1h
1xxhI01
I:5-178
1i
1xxhE01
E:2-167
1j
1xxhJ01
J:2-167
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helicase, Ruva Protein; domain 3
(218)
Homologous Superfamily
:
[code=1.10.8.60, no name defined]
(73)
Escherichia coli. Organism_taxid: 562.
(5)
2a
1xxhB02
B:179-241
2b
1xxhD02
D:179-241
2c
1xxhG02
G:179-241
2d
1xxhH02
H:179-241
2e
1xxhI02
I:179-241
2f
1xxhA02
A:143-213
2g
1xxhF02
F:143-213
2h
1xxhC02
C:179-241
Homologous Superfamily
:
DNA helicase RuvA subunit, C-terminal domain
(65)
Escherichia coli. Organism_taxid: 562.
(4)
3a
1xxhE02
E:168-207
3b
1xxhJ02
J:168-207
Architecture
:
Up-down Bundle
(3216)
Topology
:
Zinc Finger, Delta Prime; domain 3
(17)
Homologous Superfamily
:
[code=1.20.272.10, no name defined]
(16)
Escherichia coli. Organism_taxid: 562.
(1)
4a
1xxhE03
E:208-334
4b
1xxhJ03
J:208-334
4c
1xxhB03
B:242-363
4d
1xxhG03
G:242-363
4e
1xxhC03
C:242-368
4f
1xxhD03
D:242-368
4g
1xxhH03
H:242-368
4h
1xxhI03
I:242-368
Homologous Superfamily
:
[code=1.20.272.20, no name defined]
(3)
Escherichia coli. Organism_taxid: 562.
(1)
5a
1xxhA03
A:214-338
5b
1xxhF03
F:214-338
[
close CATH info
]
Pfam Domains
(4, 18)
Info
all PFAM domains
1a: PFAM_DNA_pol3_delta_1xxhF01 (F:21-190)
1b: PFAM_DNA_pol3_delta_1xxhF02 (F:21-190)
2a: PFAM_DNA_pol3_delta2_1xxhI01 (I:20-179)
2b: PFAM_DNA_pol3_delta2_1xxhI02 (I:20-179)
2c: PFAM_DNA_pol3_delta2_1xxhI03 (I:20-179)
2d: PFAM_DNA_pol3_delta2_1xxhI04 (I:20-179)
2e: PFAM_DNA_pol3_delta2_1xxhI05 (I:20-179)
2f: PFAM_DNA_pol3_delta2_1xxhI06 (I:20-179)
2g: PFAM_DNA_pol3_delta2_1xxhJ01 (J:9-168)
2h: PFAM_DNA_pol3_delta2_1xxhJ02 (J:9-168)
3a: PFAM_DNA_pol3_gamma3_1xxhI07 (I:232-368)
3b: PFAM_DNA_pol3_gamma3_1xxhI08 (I:232-368)
3c: PFAM_DNA_pol3_gamma3_1xxhI09 (I:232-368)
3d: PFAM_DNA_pol3_gamma3_1xxhI10 (I:232-368)
3e: PFAM_DNA_pol3_gamma3_1xxhI11 (I:232-368)
3f: PFAM_DNA_pol3_gamma3_1xxhI12 (I:232-368)
4a: PFAM_DNApol3_delta_C_1xxhJ03 (J:206-323)
4b: PFAM_DNApol3_delta_C_1xxhJ04 (J:206-323)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
DNA_pol3_delta
(5)
Escherichia coli (strain K12)
(5)
1a
DNA_pol3_delta-1xxhF01
F:21-190
1b
DNA_pol3_delta-1xxhF02
F:21-190
Family
:
DNA_pol3_delta2
(6)
Escherichia coli (strain K12)
(5)
2a
DNA_pol3_delta2-1xxhI01
I:20-179
2b
DNA_pol3_delta2-1xxhI02
I:20-179
2c
DNA_pol3_delta2-1xxhI03
I:20-179
2d
DNA_pol3_delta2-1xxhI04
I:20-179
2e
DNA_pol3_delta2-1xxhI05
I:20-179
2f
DNA_pol3_delta2-1xxhI06
I:20-179
2g
DNA_pol3_delta2-1xxhJ01
J:9-168
2h
DNA_pol3_delta2-1xxhJ02
J:9-168
Clan
:
no clan defined [family: DNA_pol3_gamma3]
(5)
Family
:
DNA_pol3_gamma3
(5)
Escherichia coli (strain K12)
(5)
3a
DNA_pol3_gamma3-1xxhI07
I:232-368
3b
DNA_pol3_gamma3-1xxhI08
I:232-368
3c
DNA_pol3_gamma3-1xxhI09
I:232-368
3d
DNA_pol3_gamma3-1xxhI10
I:232-368
3e
DNA_pol3_gamma3-1xxhI11
I:232-368
3f
DNA_pol3_gamma3-1xxhI12
I:232-368
Clan
:
no clan defined [family: DNApol3-delta_C]
(3)
Family
:
DNApol3-delta_C
(3)
Escherichia coli (strain K12)
(3)
4a
DNApol3-delta_C-1xxhJ03
J:206-323
4b
DNApol3-delta_C-1xxhJ04
J:206-323
[
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 (574 KB)
Header - Asym.Unit
Biol.Unit 1 (288 KB)
Header - Biol.Unit 1
Biol.Unit 2 (285 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
1XXH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help