3D1G: Small molecule inhibitor

Structure of a small molecule inhibitor bound to a DNA sliding clamp. Determined by X-ray diffraction at 1.64 Å resolution. Released 29 Jul 2008.

Method: X-ray diffraction
Resolution: 1.64 Å
Organism: Escherichia coli
Chains: 2
Atoms: 6,533
Mol. weight: 82.26 kDa
Ligands: 322
Released: 29 Jul 2008

Explore 3D1G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D1G contains 29 α-helices and 51 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	7-17	11
α-helix	28-31	4
β-strand	32-38	7	2
β-strand	41-47	7	2
β-strand	51-58	8	2
β-strand	64	1	1
β-strand	66-71	6	2
α-helix	72-81	10
α-helix	83	1
β-strand	87-93	7	1
β-strand	96-101	6	1
β-strand	104-109	6	1
β-strand	111	1	2
α-helix	113-115	3
α-helix	119-121	3
β-strand	126-130	5	2
α-helix	132-142	11
α-helix	143-145	3
α-helix	153-155	3
β-strand	157-172	16	3
β-strand	176-196	21	3
α-helix	197-205	9
β-strand	214-218	5	2
β-strand	222-227	6	2
β-strand	230-235	6	2
α-helix	236-237	2
α-helix	244-247	4
β-strand	254-259	6	3
α-helix	260-272	13
β-strand	280-286	7	4
β-strand	289-295	7	4
β-strand	301-307	7	4
β-strand	309	1	3
β-strand	315-320	6	4
α-helix	321-330	10
β-strand	335-340	6	3
β-strand	347-351	5	3
β-strand	354-361	8	3
β-strand	364	1	4

Chain B: 15 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
α-helix	8-18	11
α-helix	28-31	4
β-strand	32-38	7	5
β-strand	41-47	7	5
β-strand	51-58	8	5
β-strand	64	1	4
β-strand	66-71	6	5
α-helix	72-81	10
α-helix	83	1
β-strand	87-93	7	4
β-strand	96-101	6	4
β-strand	104-109	6	4
β-strand	111	1	5
α-helix	113-115	3
α-helix	119-121	3
β-strand	124-130	7	5
α-helix	132-142	11
α-helix	143-145	3
α-helix	153-156	4
β-strand	158-172	15	6
β-strand	176-195	20	6
α-helix	197-206	10
β-strand	214-219	6	5
β-strand	222-227	6	5
β-strand	230-235	6	5
α-helix	236-237	2
α-helix	244-246	3
α-helix	249	1
β-strand	254-259	6	6
α-helix	260-272	13
β-strand	280-286	7	1
β-strand	289-295	7	1
β-strand	301-307	7	1
β-strand	309	1	6
β-strand	315-320	6	1
α-helix	321-330	10
β-strand	335-340	6	6
β-strand	347-351	5	6
β-strand	354-361	8	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase III subunit beta	A, B	protein	366	Escherichia coli	P0A988 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3D1G_1 DNA polymerase III subunit beta (chains A, B)
MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALV
QPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD
DWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVC
SMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGR
FPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQE
EAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYV
VMPMRL

Ligands and cofactors

ID	Name	Formula	Copies
322	[(5R)-5-(2,3-dibromo-5-ethoxy-4-hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3…	C14 H13 Br2 N O5 S2	2

Primary citation

Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp. Georgescu, R.E., Yurieva, O., Kim, S.S. et al. Proc Natl Acad Sci U S A (2008) 105:11116-11121. DOI 10.1073/pnas.0804754105 · PubMed

Other PDB entries of the same protein (UniProt P0A988 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PAY 1.21 Å, Structure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 2.
8PAT 1.45 Å, Structure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 3.
4K3L 1.5 Å, E. coli sliding clamp in complex with AcLF dipeptide
8CIY 1.54 Å, DNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with…
7AZ8 1.61 Å, DNA polymerase sliding clamp from Escherichia coli with peptide 43 bound
4MJR 1.62 Å, E. coli sliding clamp in complex with (S)-Carprofen
6FVM 1.63 Å, Mutant DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide
1OK7 1.65 Å, A Conserved protein binding-site on Bacterial Sliding Clamps
7AZ7 1.65 Å, DNA polymerase sliding clamp from Escherichia coli with peptide 37 bound
4N96 1.7 Å, E. coli sliding clamp in complex with 6-nitroindazole
4N98 1.7 Å, E. coli sliding clamp in complex with 4'-fluorobiphenyl-4-carboxylic acid
4MJQ 1.73 Å, E. coli sliding clamp in complex with Bromfenac

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