7AZ8: Beta sliding clamp

DNA polymerase sliding clamp from Escherichia coli with peptide 43 bound. Determined by X-ray diffraction at 1.61 Å resolution. Released 1 Dec 2021.

Method: X-ray diffraction
Resolution: 1.61 Å
Organisms: Escherichia coli 2-427-07_S4_C3, synthetic construct
Chains: 4
Atoms: 7,051
Mol. weight: 88.91 kDa
Released: 1 Dec 2021

Explore 7AZ8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7AZ8 contains 34 α-helices and 53 β-strands across 4 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: 16 helices, 27 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	197-206	10
α-helix	212-213	2
β-strand	214-218	5	2
β-strand	222-227	6	2
β-strand	230-235	6	2
α-helix	236	1
β-strand	237	1	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

Chain B: 16 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
α-helix	7-17	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	124-131	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
α-helix	212	1
β-strand	213-219	7	5
β-strand	222-227	6	5
β-strand	230-235	6	5
α-helix	236-238	3
α-helix	244-247	4
α-helix	249	1
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	1	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
β-strand	364	1	1

Chains H and I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	103-105	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta sliding clamp	A, B	protein	386	Escherichia coli 2-427-07_S4_C3	P0A988 (AlphaFold model)
Peptide 43	H, I	protein	7	synthetic construct

Sequence of entity 1 (A, B), FASTA

>7AZ8_1 Beta sliding clamp (chains A, B)
MGSSHHHHHHSSGLVPRGSHMKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADG
TLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVR
SGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLF
ETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGS
NNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRG
VRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMML
TDSVSSVQIEDAASQSAAYVVMPMRL

Sequence of entity 2 (H, I), FASTA

>7AZ8_2 Peptide 43 (chains H, I)
XQADLPL

Primary citation

Iterative Structure-Based Optimization of Short Peptides Targeting the Bacterial Sliding Clamp. Monsarrat, C., Compain, G., Andre, C. et al. J Med Chem (2021) 64:17063-17078. DOI 10.1021/acs.jmedchem.1c00918 · 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…
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

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