8PAY: Beta sliding clamp

Structure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 2. Determined by X-ray diffraction at 1.21 Å resolution. Released 13 Mar 2024.

Method: X-ray diffraction
Resolution: 1.21 Å
Organism: Escherichia coli
Chains: 2
Atoms: 3,544
Mol. weight: 42.81 kDa
Released: 13 Mar 2024

Explore 8PAY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PAY contains 16 α-helices and 28 β-strands across 1 chain. 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: 16 helices, 28 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	124-130	7	2
α-helix	132-140	9
α-helix	143-145	3
α-helix	153-155	3
β-strand	157-163	7	3
β-strand	166-172	7	3
β-strand	176-183	8	3
β-strand	191-196	6	3
α-helix	197-206	10
α-helix	213	1
β-strand	214-219	6	2
β-strand	222-227	6	2
β-strand	230-235	6	2
α-helix	236-238	3
α-helix	244-247	4
α-helix	249	1
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
β-strand	364	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta sliding clamp	A	protein	370	Escherichia coli	P0A988 (AlphaFold model)
Ace-gln-alc-glc-leu-phe	H	protein	6	Escherichia coli

Sequence of entity 1 (A), FASTA

>8PAY_1 Beta sliding clamp (chains A)
PGSHMKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVAR
VALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADF
PNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHR
LAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKL
VDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANN
PEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQS
AAYVVMPMRL

Sequence of entity 2 (H), FASTA

>8PAY_2 ACE-GLN-ALC-GLC-LEU-PHE (chains H)
XQAXLF

Primary citation

Peptide-Based Covalent Inhibitors Bearing Mild Electrophiles to Target a Conserved His Residue of the Bacterial Sliding Clamp. Compain, G., Monsarrat, C., Blagojevic, J. et al. JACS Au (2024) 4:432-440. DOI 10.1021/jacsau.3c00572 · PubMed

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

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
4MJQ 1.73 Å, E. coli sliding clamp in complex with Bromfenac

Browse structure collections

About this viewer

MolViewer shows 8PAY 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.