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3D1F
Biol. Unit 1
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Asym.Unit (136 KB)
Biol.Unit 1 (132 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF E. COLI SLIDING CLAMP (BETA) BOUND TO A POLYMERASE III PEPTIDE
Authors
:
R. E. Georgescu, O. Yurieva, K. Seung-Sup, J. Kuriyan, X-P. Kong, M. O'Donnell
Date
:
05 May 08 (Deposition) - 29 Jul 08 (Release) - 09 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,P,Q
Biol. Unit 1: A,B,P,Q (1x)
Keywords
:
Chemical Probe, Dna Polymerase, Dna Sliding Clamp, Dna Replication, Rational Drug Design, Antibiotic Target, Transferase, Transcription
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. E. Georgescu, O. Yurieva, S. S. Kim, J. Kuriyan, X. P. Kong, M. O'Donnell
Structure Of A Small-Molecule Inhibitor Of A Dna Polymerase Sliding Clamp.
Proc. Natl. Acad. Sci. Usa V. 105 11116 2008
(for further references see the
PDB file header
)
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: 2-[3,6-BIS(DIMETHYLAMINO)XANTHEN-9... (323a)
1b: 2-[3,6-BIS(DIMETHYLAMINO)XANTHEN-9... (323b)
2a: DI(HYDROXYETHYL)ETHER (PEGa)
2b: DI(HYDROXYETHYL)ETHER (PEGb)
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No.
Name
Count
Type
Full Name
1
323
2
Ligand/Ion
2-[3,6-BIS(DIMETHYLAMINO)XANTHEN-9-YL]-5-METHANOYL-BENZOATE
2
PEG
2
Ligand/Ion
DI(HYDROXYETHYL)ETHER
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Sites
(4, 4)
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1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:365 , SER P:2 , GLU P:3
BINDING SITE FOR RESIDUE 323 P 1
2
AC2
SOFTWARE
ARG B:365 , SER Q:2 , GLU Q:3
BINDING SITE FOR RESIDUE 323 Q 1
3
AC3
SOFTWARE
GLU A:6 , HIS A:9 , ASN B:221 , ASP B:238
BINDING SITE FOR RESIDUE PEG A 367
4
AC4
SOFTWARE
LYS A:12
BINDING SITE FOR RESIDUE PEG A 368
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SAPs(SNPs)/Variants
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3d1fa1 (A:1-122)
1b: SCOP_d3d1fa2 (A:123-244)
1c: SCOP_d3d1fa3 (A:245-366)
1d: SCOP_d3d1fb1 (B:1-122)
1e: SCOP_d3d1fb2 (B:123-244)
1f: SCOP_d3d1fb3 (B:245-366)
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Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
DNA clamp
(88)
Superfamily
:
DNA clamp
(88)
Family
:
DNA polymerase III, beta subunit
(31)
Protein domain
:
DNA polymerase III, beta subunit
(31)
Escherichia coli [TaxId: 562]
(30)
1a
d3d1fa1
A:1-122
1b
d3d1fa2
A:123-244
1c
d3d1fa3
A:245-366
1d
d3d1fb1
B:1-122
1e
d3d1fb2
B:123-244
1f
d3d1fb3
B:245-366
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_3d1fA01 (A:1-123)
1b: CATH_3d1fA03 (A:248-366)
1c: CATH_3d1fB03 (B:248-366)
1d: CATH_3d1fB01 (B:1-123)
1e: CATH_3d1fA02 (A:124-247)
1f: CATH_3d1fB02 (B:124-247)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
DNA Polymerase III; Chain A, domain 2
(13)
Homologous Superfamily
:
DNA Polymerase III, subunit A, domain 2
(13)
Escherichia coli. Strain: k12.
(2)
1a
3d1fA01
A:1-123
1b
3d1fA03
A:248-366
1c
3d1fB03
B:248-366
1d
3d1fB01
B:1-123
1e
3d1fA02
A:124-247
1f
3d1fB02
B:124-247
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Pfam Domains
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Asym.Unit (136 KB)
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