4N95: E. coli sliding clamp

E. coli sliding clamp in complex with 5-chloroindoline-2,3-dione. Determined by X-ray diffraction at 1.8 Å resolution. Released 6 Nov 2013.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Escherichia coli
Chains: 2
Atoms: 6,323
Mol. weight: 82.71 kDa
Ligands: CA, 2HQ
Released: 6 Nov 2013

Explore 4N95 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4N95 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	4
α-helix	7-18	12
α-helix	29-31	3
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	124-131	8	5
α-helix	132-142	11
α-helix	143-145	3
α-helix	153-155	3
β-strand	157-172	16	6
β-strand	176-196	21	6
α-helix	197-206	10
β-strand	213-219	7	5
β-strand	222-227	6	5
β-strand	230-235	6	5
α-helix	236	1
β-strand	237	1	6
α-helix	244-246	3
β-strand	254-259	6	6
α-helix	260-271	12
β-strand	280-286	7	1
β-strand	289-295	7	1
β-strand	301-307	7	1
β-strand	309-311	3	6
β-strand	315-320	6	1
α-helix	321-331	11
β-strand	335-340	6	6
β-strand	347-351	5	6
β-strand	357-361	5	6

Chain B: 15 helices, 25 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
α-helix	213	1
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	244-246	3
β-strand	254-259	6	3
α-helix	260-271	12
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	321-331	11
β-strand	335-340	6	3
β-strand	347-351	5	3
β-strand	357-361	5	3

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

>4N95_1 DNA polymerase III subunit beta (chains A, B)
MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALV
QPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD
DWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVC
SMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGR
FPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQE
EAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYV
VMPMRL

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
2HQ	5-chloro-1H-indole-2,3-dione	C8 H4 Cl N O2	1

Water and common crystallization additives (PGE, CL, PEG, PG4) are not listed.

Primary citation

Discovery of lead compounds targeting the bacterial sliding clamp using a fragment-based approach. Yin, Z., Whittell, L.R., Wang, Y. et al. J Med Chem (2014) 57:2799-2806. DOI 10.1021/jm500122r · 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
3D1G 1.64 Å, Structure of a small molecule inhibitor bound to a DNA sliding clamp
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

Browse structure collections

About this viewer

MolViewer shows 4N95 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.