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1XXI
Asym. Unit
Info
Asym.Unit (486 KB)
Biol.Unit 1 (242 KB)
Biol.Unit 2 (242 KB)
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(1)
Title
:
ADP 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) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
4.10
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, 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 Escherichia Coli Dna Polymerase Clamp-Loader Complex
Proc. Natl. Acad. Sci. Usa V. 101 16750 2004
(for further references see the
PDB file header
)
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
2a: PHOSPHATE ION (PO4a)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
3
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
PO4
1
Ligand/Ion
PHOSPHATE ION
3
ZN
8
Ligand/Ion
ZINC ION
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Sites
(12, 12)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
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
02
AC2
SOFTWARE
CYS C:64 , CYS C:73 , CYS C:76 , CYS C:79
BINDING SITE FOR RESIDUE ZN C 401
03
AC3
SOFTWARE
CYS D:64 , CYS D:73 , GLY D:74 , CYS D:76 , CYS D:79
BINDING SITE FOR RESIDUE ZN D 402
04
AC4
SOFTWARE
CYS B:64 , CYS B:73 , GLY B:74 , CYS B:76 , CYS B:79
BINDING SITE FOR RESIDUE ZN B 403
05
AC5
SOFTWARE
CYS E:50 , CYS E:59 , CYS E:62 , CYS E:65
BINDING SITE FOR RESIDUE ZN E 404
06
AC6
SOFTWARE
CYS H:64 , CYS H:73 , CYS H:76 , CYS H:79
BINDING SITE FOR RESIDUE ZN H 405
07
AC7
SOFTWARE
CYS I:64 , CYS I:73 , GLY I:74 , CYS I:76 , CYS I:79
BINDING SITE FOR RESIDUE ZN I 406
08
AC8
SOFTWARE
CYS G:64 , CYS G:73 , GLY G:74 , CYS G:76 , CYS G:79
BINDING SITE FOR RESIDUE ZN G 407
09
AC9
SOFTWARE
CYS J:50 , CYS J:59 , CYS J:62 , CYS J:65
BINDING SITE FOR RESIDUE ZN J 408
10
BC1
SOFTWARE
ALA D:7 , TRP D:10 , ARG D:11 , PRO D:12 , VAL D:19 , GLY D:48 , VAL D:49 , GLY D:50 , LYS D:51 , THR D:52 , SER D:53 , LEU D:214 , ARG D:215 , LEU D:218
BINDING SITE FOR RESIDUE ADP D 801
11
BC2
SOFTWARE
ALA B:7 , TRP B:10 , ARG B:11 , PRO B:12 , VAL B:18 , VAL B:19 , GLY B:48 , VAL B:49 , GLY B:50 , LYS B:51 , THR B:52 , SER B:53 , LEU B:214 , ARG B:215 , LEU B:218
BINDING SITE FOR RESIDUE ADP B 802
12
BC3
SOFTWARE
ALA I:7 , TRP I:10 , ARG I:11 , VAL I:18 , VAL I:19 , GLY I:48 , VAL I:49 , GLY I:50 , LYS I:51 , THR I:52 , SER I:53 , LEU I:214 , ARG I:215 , LEU I:218
BINDING SITE FOR RESIDUE ADP I 803
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
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Exons
(0, 0)
Info
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(6, 20)
Info
All SCOP Domains
1a: SCOP_d1xxie1 (E:208-334)
1b: SCOP_d1xxij1 (J:208-334)
2a: SCOP_d1xxia1 (A:212-338)
2b: SCOP_d1xxif1 (F:212-338)
3a: SCOP_d1xxib1 (B:243-368)
3b: SCOP_d1xxic1 (C:243-368)
3c: SCOP_d1xxid1 (D:243-368)
3d: SCOP_d1xxig1 (G:243-368)
3e: SCOP_d1xxih1 (H:243-368)
3f: SCOP_d1xxii1 (I:243-368)
4a: SCOP_d1xxie2 (E:1-207)
4b: SCOP_d1xxij2 (J:1-207)
5a: SCOP_d1xxia2 (A:1-211)
5b: SCOP_d1xxif2 (F:1-211)
6a: SCOP_d1xxib2 (B:5-242)
6b: SCOP_d1xxic2 (C:5-242)
6c: SCOP_d1xxid2 (D:5-242)
6d: SCOP_d1xxig2 (G:5-242)
6e: SCOP_d1xxih2 (H:5-242)
6f: SCOP_d1xxii2 (I:5-242)
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Classes
(
)
(
)
Folds
(
)
(
)
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(
)
(
)
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
d1xxie1
E:208-334
1b
d1xxij1
J:208-334
Protein domain
:
delta subunit
(4)
Escherichia coli [TaxId: 562]
(4)
2a
d1xxia1
A:212-338
2b
d1xxif1
F:212-338
Protein domain
:
gamma subunit
(4)
Escherichia coli [TaxId: 562]
(3)
3a
d1xxib1
B:243-368
3b
d1xxic1
C:243-368
3c
d1xxid1
D:243-368
3d
d1xxig1
G:243-368
3e
d1xxih1
H:243-368
3f
d1xxii1
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
d1xxie2
E:1-207
4b
d1xxij2
J:1-207
Protein domain
:
delta subunit of DNA polymerase III, N-domain
(5)
Escherichia coli [TaxId: 562]
(5)
5a
d1xxia2
A:1-211
5b
d1xxif2
F:1-211
Protein domain
:
gamma subunit of DNA polymerase III, N-domain
(4)
Escherichia coli [TaxId: 562]
(3)
6a
d1xxib2
B:5-242
6b
d1xxic2
C:5-242
6c
d1xxid2
D:5-242
6d
d1xxig2
G:5-242
6e
d1xxih2
H:5-242
6f
d1xxii2
I:5-242
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(4, 18)
Info
all PFAM domains
1a: PFAM_DNA_pol3_delta_1xxiF01 (F:21-190)
1b: PFAM_DNA_pol3_delta_1xxiF02 (F:21-190)
2a: PFAM_DNA_pol3_delta2_1xxiI01 (I:20-179)
2b: PFAM_DNA_pol3_delta2_1xxiI02 (I:20-179)
2c: PFAM_DNA_pol3_delta2_1xxiI03 (I:20-179)
2d: PFAM_DNA_pol3_delta2_1xxiI04 (I:20-179)
2e: PFAM_DNA_pol3_delta2_1xxiI05 (I:20-179)
2f: PFAM_DNA_pol3_delta2_1xxiI06 (I:20-179)
2g: PFAM_DNA_pol3_delta2_1xxiJ01 (J:9-168)
2h: PFAM_DNA_pol3_delta2_1xxiJ02 (J:9-168)
3a: PFAM_DNA_pol3_gamma3_1xxiI07 (I:232-368)
3b: PFAM_DNA_pol3_gamma3_1xxiI08 (I:232-368)
3c: PFAM_DNA_pol3_gamma3_1xxiI09 (I:232-368)
3d: PFAM_DNA_pol3_gamma3_1xxiI10 (I:232-368)
3e: PFAM_DNA_pol3_gamma3_1xxiI11 (I:232-368)
3f: PFAM_DNA_pol3_gamma3_1xxiI12 (I:232-368)
4a: PFAM_DNApol3_delta_C_1xxiJ03 (J:206-323)
4b: PFAM_DNApol3_delta_C_1xxiJ04 (J:206-323)
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)
(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
DNA_pol3_delta
(5)
Escherichia coli (strain K12)
(5)
1a
DNA_pol3_delta-1xxiF01
F:21-190
1b
DNA_pol3_delta-1xxiF02
F:21-190
Family
:
DNA_pol3_delta2
(6)
Escherichia coli (strain K12)
(5)
2a
DNA_pol3_delta2-1xxiI01
I:20-179
2b
DNA_pol3_delta2-1xxiI02
I:20-179
2c
DNA_pol3_delta2-1xxiI03
I:20-179
2d
DNA_pol3_delta2-1xxiI04
I:20-179
2e
DNA_pol3_delta2-1xxiI05
I:20-179
2f
DNA_pol3_delta2-1xxiI06
I:20-179
2g
DNA_pol3_delta2-1xxiJ01
J:9-168
2h
DNA_pol3_delta2-1xxiJ02
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_gamma3-1xxiI07
I:232-368
3b
DNA_pol3_gamma3-1xxiI08
I:232-368
3c
DNA_pol3_gamma3-1xxiI09
I:232-368
3d
DNA_pol3_gamma3-1xxiI10
I:232-368
3e
DNA_pol3_gamma3-1xxiI11
I:232-368
3f
DNA_pol3_gamma3-1xxiI12
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-1xxiJ03
J:206-323
4b
DNApol3-delta_C-1xxiJ04
J:206-323
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Asym.Unit (486 KB)
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